Compositions and kits for molecular counting

ABSTRACT

Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/603,921 filed Feb. 27, 2012, and U.S. Provisional Application No.61/745,385, filed Dec. 21, 2012, both of which are incorporated byreference herein in their entirety.

FIELD OF THE INVENTION

Methods and uses of molecular counting are disclosed. Molecules can becounted by sequencing and tracking the number of occurrences of a targetmolecule. Molecules can also be counted by hybridization of the moleculeto a solid support and detection of the hybridized molecules. In someinstances, the molecules to be counted are labeled. The molecules to becounted may also be amplified.

BACKGROUND OF THE INVENTION

Accurate determination of the quantity of nucleic acids is necessary ina wide variety of clinical and research measurements. When dissolved insolution, the average concentration of nucleic acids (RNA or DNA) can bedetermined by UV light absorbance spectrophotometry or by fluorescentDNA-binding stains. However, the measurement required is often not justfor the total amount of nucleic acids present, but specifically for oneor more species of interest contained and mixed with all of the othernucleic acids within the sample. In these cases, the nucleic acidmolecule of interest is usually distinguished from all of the othernucleic acids through a defined sequence of nucleotides that is uniqueto the species of interest. A short synthetic ribo- ordeoxyribo-oligonucleotide with a complementary sequence to the nucleicacid of interest can be used for its detection and identification. Forinstance, the Polymerase Chain Reaction (PCR) uses a pair of theseoligonucleotides to serve as annealing primers for repeated cycles ofDNA polymerization mediated by DNA polymerase enzymes. DNA microarraysare another common detection method where oligonucleotides areimmobilized on solid supports to hybridize to DNA molecules bearingcomplementary sequences. Although both PCR and microarray methods arecapable of specific detection, accurate determination of the quantity ofthe detected molecules is difficult (especially when it is present inlow abundance or when contained within a large background of othernucleic acids). In the case of PCR (also sometimes referred to asquantitative-PCR, qPCR, TaqMan, or real-time PCR), the amount ofamplified DNA molecules represents an estimate of its concentration inthe starting solution. In the case of micro arrays, the amount of DNAhybridized is an estimate of its concentration in solution. In bothcases, only relative measurements of concentration can be made, and theabsolute number of copies of nucleic acid in the sample cannot beprecisely determined. However, when reference nucleic acids ofpre-determined concentrations are included in the test, relativecomparisons can be made to this standard reference to estimate theabsolute number of copies of nucleic acids being detected.

Digital PCR is one method that can be used to determine the absolutenumber of DNA molecules of a particular nucleotide sequence (Sykes etal. Biotechniques 13: 444-449 (1992), Vogelstein et al. Digital PCR.Proc Natl Acad Sci USA 96: 9236-9241 (1999)). In this method, thenucleic acid solution is diluted and stochastically partitioned intoindividual containers so that there is on average less than one moleculein every two containers. PCR is then used to detect the presence of thenucleic acid molecule of interest in each container. If quantitativepartitioning is assumed, the dynamic range is governed by the number ofcontainers available for stochastic separation. Micro fabrication andpicoliter-sized emulsion droplets can be used to increase the number ofcontainers available thereby extending the measurement dynamic range(Fan et al. Am J Obstet Gynecol 200: 543 e541-547 (2009), Kalinina etal. Nucleic Acids Res 25: 1999-2004 (1997)). Due to the physicalconstraints of manufacturing large numbers of separate containers and incarrying out these larger numbers of reactions, in practice the digitalPCR method is limited to investigations on only a small number ofdifferent DNA molecules at a time.

Recently, a new method to determine the absolute quantity of DNAmolecules has been demonstrated where identical copies of individual DNAmolecules can be counted after the stochastic attachment of a set ofdiverse nucleic acid labels (Fu et al. Proc Natl Acad Sci USA 108:9026-9031 (2011)). Unlike digital PCR, this is a highly parallel methodcapable of counting many different DNA molecules simultaneously. In thismethod, each copy of a molecule randomly attaches to a short nucleicacid label by choosing from a large, non-depleting reservoir of diverselabels. The subsequent diversity of the labeled molecules is governed bythe statistics of random choice, and depends on the number of copies ofidentical molecules in the collection compared to the number of kinds oflabels. Once the molecules are labeled, they can be amplified so thatsimple present/absent threshold detection methods can be used for each.Counting the number of distinctly labeled targets reveals the originalnumber of molecules of each species. Unlike digital PCR, whichstochastically expands identical molecules into physical space, themethod of stochastic labeling expands identical molecules into chemicalspace. An important distinction from digital PCR is that the stochasticlabeling method does not require the challenging physical separation ofidentical molecules into individual physical containers. The approach ispractical, and after labeling, a simple detector device such as amicroarray with complementary probe sequences to the labels can be usedto identify and count the number of labels present. In addition, whenstochastic labels are attached to DNA molecules that are prepared forDNA sequencing readouts, the labeling sequence can serve as discreetcounting tags for absolute quantitation, or as unique identifiers todistinguish each originally tagged template from its amplified daughtermolecules (Kinde et al. Proc Natl Acad Sci USA 108: 9530-9535 (2011)).

SUMMARY OF THE INVENTION

In some embodiments is a digital reverse transcription methodcomprising: a) contacting a sample comprising a plurality of RNAmolecules with a plurality of oligonucleotide tags to produce alabeled-RNA molecule, wherein: the plurality of RNA molecules compriseat least 2 mRNA molecules of different sequences; the plurality ofoligonucleotide tags comprises at least 2 oligonucleotide tags ofdifferent sequences; and the plurality of oligonucleotide tags comprisesan oligodT sequence; b) conducting a first strand synthesis reaction bycontacting the labeled-RNA molecules with a reverse transcriptase enzymeto produce a labeled-cDNA molecule; and c) detecting the labeled-cDNAmolecule by hybridizing the labeled-cDNA molecule to a solid support.

In some embodiments is a stochastic label-based hybridization chainreaction method comprising stochastically labeling one or more nucleicacid molecules with a plurality of hairpin oligonucleotide tags, whereinthe hairpin oligonucleotide tag comprises an overhang; and the one ormore nucleic acid molecules act as initiators for a hybridization chainreaction.

At least a portion of the hairpin oligonucleotide tag may hybridize toat least a portion of the one or more nucleic acid molecules. Thehairpin oligonucleotide tag may comprise an oligodT sequence. The one ormore nucleic acid molecules may comprise one or more adapters. At leasta portion of the hairpin oligonucleotide tag may hybridize to at least aportion of the one or more adapters. At least one hairpinoligonucleotide tag of the plurality of hairpin oligonucleotide tags maycomprise one or more labels. At least one hairpin oligonucleotide tag ofthe plurality of hairpin oligonucleotide tags may comprise two or morelabels.

Each hairpin oligonucleotide tag of the plurality of hairpinoligonucleotide tags may comprise one or more labels. Each hairpinoligonucleotide tag of the plurality of hairpin oligonucleotide tags maycomprise two or more labels. In some instances, the hairpinoligonucleotide tag does not comprise a label.

The plurality of hairpin oligonucleotide tags may comprise one or morehairpin oligonucleotide tags with a 5′ overhang, hairpin oligonucleotidetags with a 3′ overhang, or a combination thereof.

The stem portion of the hairpin oligonucleotide tag can be one or morenucleotides in length. The stem portion of the hairpin oligonucleotidetag can be two or more nucleotides in length. The stem portion of thehairpin oligonucleotide tag can be three or more nucleotides in length.The stem portion of the hairpin oligonucleotide tag can be four or morenucleotides in length. The stem portion of the hairpin oligonucleotidetag can be five or more nucleotides in length. The stem portion of thehairpin oligonucleotide tag can be six or more nucleotides in length.The stem portion of the hairpin oligonucleotide tag can be seven or morenucleotides in length. The stem portion of the hairpin oligonucleotidetag can be eight or more nucleotides in length. The stem portion of thehairpin oligonucleotide tag can be nine or more nucleotides in length.The stem portion of the hairpin oligonucleotide tag can be ten or morenucleotides in length. The stem portion of the hairpin oligonucleotidetag can be 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or morenucleotides in length.

The loop portion of the hairpin oligonucleotide tag can be one or morenucleotides in length. The loop portion of the hairpin oligonucleotidetag can be two or more nucleotides in length. The loop portion of thehairpin oligonucleotide tag can be three or more nucleotides in length.The loop portion of the hairpin oligonucleotide tag can be four or morenucleotides in length. The loop portion of the hairpin oligonucleotidetag can be five or more nucleotides in length. The loop portion of thehairpin oligonucleotide tag can be six or more nucleotides in length.The loop portion of the hairpin oligonucleotide tag can be seven or morenucleotides in length. The loop portion of the hairpin oligonucleotidetag can be eight or more nucleotides in length. The loop portion of thehairpin oligonucleotide tag can be nine or more nucleotides in length.The loop portion of the hairpin oligonucleotide tag can be ten or morenucleotides in length. The loop portion of the hairpin oligonucleotidetag can be 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or morenucleotides in length.

The hairpin oligonucleotide tag may comprise a unique identifier region.The unique identifier region can be in the loop portion of the hairpinoligonucleotide tag. The unique identifier region can be in the stemportion of the hairpin oligonucleotide tag. The unique identifier regioncan be in the overhang portion of the hairpin oligonucleotide tag.

The label may comprise a unique identifier region.

In some embodiments the oligonucleotide tag further comprises a uniqueidentifier region. In some embodiments the unique identifier region isat least one nucleotide in length. In some embodiments theoligonucleotide tag further comprises a universal primer binding site.In some embodiments the oligonucleotide tag is at least one nucleotidein length.

In some embodiments the solid support is an array. In some embodimentsthe solid support is an addressable array. In some embodiments the solidsupport is an Affymetrix 3K tag array, Arrayjet non-contact printedarray, or Applied Microarrays Inc (AMI) array. In some embodiments thesolid support is a bead.

Further disclosed herein is cell analysis method comprising: a)contacting a sample comprising a plurality of molecules with a pluralityof oligonucleotide tags to produce a labeled-molecule, wherein: theplurality of molecules comprise at least 2 molecules of differentsequences; the plurality of oligonucleotide tags comprises at least 2oligonucleotide tags of different sequences; and the sample is from atleast one cell; and b) detecting the labeled-molecule by hybridizing thelabeled-molecule to a solid support.

In some embodiments is a clonal amplification method comprising: a)stochastically labeling a plurality of molecules with a plurality ofoligonucleotide tags to produce a labeled-molecule, wherein: theplurality of molecules comprise at least 2 molecules of differentsequences; and the plurality of oligonucleotide tags comprises at least2 oligonucleotide tags of different sequences; b) amplifying thelabeled-molecules to produce a labeled-amplicon; and c) detecting thelabeled-amplicon.

Further disclosed herein is a kit comprising: a) a plurality ofoligonucleotide tags, wherein the oligonucleotide tag of the pluralityof oligonucleotide tags comprises: a target specific region; and aunique identifier region; and b) an enzyme.

In some embodiments the enzyme is a reverse transcriptase enzyme. Insome embodiments the enzyme is a ligase. In some embodiments the enzymeis a polymerase. In some embodiments the enzyme is an RNase. In someembodiments the enzyme is a DNase. In some embodiments the enzyme is anendonuclease.

In some embodiments the oligonucleotide tag is at least 25 nucleotidesin length. In some embodiments the unique identifier region is at least10 nucleotides in length. In some embodiments the target specific regionis at least 10 nucleotides in length. In some embodiments the targetspecific region comprises an oligodT sequence. In some embodiments theoligonucleotide tag further comprises a universal primer binding site.

In some embodiments the kit further comprises a support. In someembodiments the support is a semi-solid support. In some embodiments thesupport is a solid support. In some embodiments the solid support is anarray. In some embodiments the support is an addressable array. In someembodiments the support is an Affymetrix 3K tag array, Arrayjetnon-contact printed array, or Applied Microarrays Inc (AMI) array. Insome embodiments the support is a bead.

In some embodiments the kit further comprises a primer. In someembodiments the primer is a universal primer. In some embodiments theprimer binds to the oligonucleotide tag. In some embodiments the primerbinds to the universal primer binding site of the oligonucleotide tag.

In some embodiments the kit further comprises a control oligo. In someembodiments the control oligo comprises at least 15 nucleotides. In someembodiments the control oligo is a bright hybridization control oligo.In some embodiments the control oligo is a spike-in template control. Insome embodiments the oligonucleotide tag further comprises a label.

In some embodiments the primer further comprises a label. In someembodiments the control oligo further comprises a label. In someembodiments the label is a dye label. In some embodiments the label is aCy3 dye. In some embodiments the label is a Tye563 dye.

In some embodiments the kit further comprises a buffer.

In some embodiments the kit further comprises a carrier.

In some embodiments the kit further comprises a detergent.

Further disclosed herein is a system for determining the absolutequantity of a plurality of nucleic acid molecules. The system maycomprise a) a plurality of oligonucleotide tags; and b) a detector fordetecting at least a portion of the oligonucleotide tags.

The detector may comprise an array detector, fluorescent reader,non-fluorescent detector, CR reader, or scanner. In some embodiments themethod further comprises the fluorescent reader is a Sensovation or AGfluorescent reader. In some embodiments the method further comprises thescanner is a flatbed scanner.

The system may further comprise a thermal cycler. In some embodimentsthe system further comprises a sequencer. In some embodiments the systemfurther comprises a hybridization chamber.

The system may further comprise a computer. In some embodiments thecomputer comprises a memory device. In some embodiments the memorydevice is capable of storing data. In some embodiments the systemfurther comprises a software program. In some embodiments the systemfurther comprises a computer-readable program.

In some embodiments the oligonucleotide tag further comprises a uniqueidentifier region. In some embodiments the unique identifier region isat least 10 nucleotides in length. In some embodiments the uniqueidentifier region cannot hybridize to the molecule. In some embodimentsthe oligonucleotide tag further comprises a universal primer bindingsite. In some embodiments the oligonucleotide tag is at least 20nucleotides in length. In some embodiments the oligonucleotide tagfurther comprises a target specific region. In some embodiments thetarget specific region comprises an oligodT sequence. In someembodiments the target specific region is at least 10 nucleotides inlength. In some embodiments the method further comprises conducting afirst strand synthesis reaction to produce a labeled-cDNA molecule.

In some embodiments the amplifying the labeled-molecule comprisesconducting a polymerase chain reaction. Alternatively, amplifying thelabeled-molecule may comprise conducting a non-PCR based amplificationreaction. Amplifying the labeled-molecule may comprise exponentialamplification of the labeled-molecule. Amplifying the labeled-moleculemay comprise linear amplification of the labeled molecule. Amplifyingthe labeled-molecule may comprise hybridization chain reaction (HCR)based amplification method.

Amplifying the labeled-molecule may comprise amplifying at least thelabel portion of the labeled molecule, the molecule portion of thelabeled molecule, or a combination thereof.

In some embodiments the method further comprises conducting a polymerasechain reaction on the labeled-molecule or any product thereof to producea double-stranded labeled-molecule. In some embodiments conducting thepolymerase chain reaction comprises annealing a first target specificprimer to the labeled-molecule or any product thereof. In someembodiments conducting the polymerase chain reaction further comprisesannealing a universal primer to the universal primer binding site of theoligonucleotide tag. In some embodiments the polymerase chain reactioncomprises absolute PCR, HD-PCR, Next Gen PCR, digital RTA, or anycombination thereof. In some embodiments the method comprises conductinga nested PCR reaction on the double-stranded labeled-cDNA molecule. Insome embodiments conducting the nested PCR reaction comprises denaturingthe labeled-molecule or any product thereof to produce a denaturedsingle-stranded labeled-molecule or any product thereof. In someembodiments conducting the nested PCR reaction further comprisesannealing a second target specific primer to the denaturedsingle-stranded labeled-molecule or any product thereof. In someembodiments conducting the nested PCR reaction further comprisesannealing a universal primer to the universal primer binding site of theoligonucleotide tag.

In some embodiments the method further comprises conducting a sequencingreaction to determine the sequence of at least a portion of theoligonucleotide tag, at least a portion of the labeled-molecule, aproduct thereof, a complement thereof, a reverse complement thereof, orany combination thereof.

In some embodiments detecting the labeled-molecules or any productsthereof comprises an array detector, fluorescent reader, non-fluorescentdetector, CR reader, or scanner. In some embodiments the molecule is anucleic acid molecule.

In some embodiments the nucleic acid molecule is a DNA molecule. In someembodiments the nucleic acid molecule is an RNA molecule. In someembodiments the molecule is a peptide. In some embodiments the peptideis a polypeptide.

In some embodiments the plurality of molecules is from a cell. In someembodiments the sample is from a single cell. In some embodiments thesample is from less than about 100 cells. In some embodiments the sampleis from less than about 50 cells. In some embodiments the sample is fromless than about 20 cells. In some embodiments the sample is from lessthan about 10 cells. In some embodiments the sample is from less thanabout 5 cells. In some embodiments the cell is a mammalian cell. In someembodiments the cell is a human cell. In some embodiments the cell isfrom a subject suffering from a disease or condition. In someembodiments the disease or condition is cancer. In some embodiments thedisease or condition is a pathogenic infection. In some embodiments thedisease or condition is a genetic disorder. In some embodiments the cellis from a healthy subject. In some embodiments the cell is a diseasedcell. In some embodiments the diseased cell is a cancerous cell. In someembodiments the cell is a healthy cell. In some embodiments the cell isnot a diseased or infected cell. In some embodiments thelabeled-molecules are produced by stochastic labeling.

BRIEF DESCRIPTION OF THE DRAWINGS

The skilled artisan will understand that the drawings described beloware for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way.

FIG. 1 shows a schematic of labeling and detection of a target molecule

FIG. 2 shows signals for the detection of labels in hybridized molecules

FIG. 3 shows signals for the detection of labels in hybridized molecules

FIG. 4 shows signals for the detection of labels in hybridized molecules

FIG. 5 shows signals for the detection of labels in hybridized molecules

FIG. 6 shows signals for the detection of labels in hybridized molecules

FIG. 7 shows a schematic of detection of a labeled molecule by an arraydetector

FIG. 8 shows a schematic of stochastic labeling of a plurality ofmolecules

FIG. 9 Exemplary PCR primer consisting of a universal PCR sequence, ashort label sequence and a target or gene-specific sequence.

FIG. 10 shows a schematic for the synthesis of oligonucleotide tags

FIG. 11A shows a schematic for the synthesis of oligonucleotide tagswithout target-specific sequence

FIG. 11B-D shows a schematic for the synthesis of oligonucleotide tags

FIG. 12A-B depict degenerate oligonucleotide tags

FIG. 13 Additional Examples of Labeled Primers. A) Labeled Primerwithout generic primer sequence. B) Labeled Primer with universal targetsequence

FIG. 14 Absolute PCR Protocol

FIG. 15 Formation of Primer Dimers

FIG. 16 Method to prevent the formation of primer artifacts

FIG. 17 Differences between a standard array and a digital array

FIG. 18 Digital microarray probes—detection using a combination of geneand label sequences

FIG. 19 Absolute quantitation of mRNA molecules by counting individualDNA molecules

FIG. 20 Digital microarray for RNA expression

FIG. 21 Digital microarray for DNA copy number

FIG. 22 Digital microarray for microRNAs

FIG. 23A Digital microarray for single cell pre-implantation geneticdiagnosis (PGD) (a) cycle 0; (b) cycle 5; (c) cycle 10; (d) cycle 15

FIG. 23B shows a schematic of a method for single cell pre-implantationgenetic diagnosis (PGD)

FIG. 24 Digital microarray for measuring fetal aneuploidy in maternalcirculating nucleic acids—e.g., Trisomy 21

FIG. 25 Absolute quantitation of mRNA molecules by counting individualDNA molecules

FIG. 26 Labeling with an “inert” primer

FIG. 27 Emulsion PCR to prevent artifacts from out-competing cDNAsduring amplification

FIG. 28 A method that does not rely on homopolymer tailing

FIG. 29 Linear amplification methods

FIG. 30 Labeling with strand switching

FIG. 31 Labeling by random priming

FIG. 32A-B show the results for the optimization of cDNA synthesis

FIG. 33 Schematic of stochastic labeling followed by HCR detection ofnucleic acid molecules

FIG. 34 Schematic of stochastic labeling of hairping HCRoligonucleotides

FIG. 35 Schematic of the serial dilution scheme for the titrationexperiment with serial dilutions of kanamycin RNA

FIG. 36A-H Shows the scatter plots of results for the titrationexperiment with serial dilutions of kanamycin RNA

FIG. 37 Shows the Correlation graph for the titration experiment withserial dilutions of kanamycin RNA

FIG. 38 Schematic of the serial dilution scheme for the titrationexperiment with serial dilutions of human liver RNA to measure GAPDHexpression

FIG. 39A-H Shows the scatter plots of results for the titrationexperiment with serial dilutions of human liver RNA to measure GAPDHexpression

FIG. 40 Shows the correlation graph for the titration experiment withserial dilutions of human liver RNA to measure GAPDH expression

FIG. 41A-D Shows the scatter plots of results for the accuratemeasurements of control bacterial genes

FIG. 42 Shows the scatter plot for the validation of kanamycin counts bydigital PCR experiment

FIG. 43 Schematic of the method for absolute quantitation of mRNAmolecules directly from cell lysates

DETAILED DESCRIPTION OF THE INVENTION

Reference will now be made in detail to exemplary embodiments of theinvention. While the invention will be described in conjunction with theexemplary embodiments, it will be understood that they are not intendedto limit the invention to these embodiments. On the contrary, theinvention is intended to cover alternatives, modifications andequivalents, which may be included within the spirit and scope of theinvention.

The invention has many preferred embodiments and relies on many patents,applications and other references for details known to those of the art.Therefore, when a patent, application, or other reference, such as aprinted publication, is cited or repeated below, it should be understoodthat it is incorporated by reference in its entirety for all purposesand particularly for the proposition that is recited.

An individual is not limited to a human being, but may also be otherorganisms including, but not limited to, mammals, plants, bacteria, orcells derived from any of the above.

Throughout this disclosure, various aspects of this invention can bepresented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Disclosed herein are methods, kits, and systems for detecting and/orquantifying molecules in a sample. In some instances, methods, kits, andsystems for individually counting molecules in a sample are provided.Alternatively, methods, kits, and systems for determining the expressionlevel of a gene or gene produce are provided. In some instances, themethods comprise the attachment of an oligonucleotide tag to a molecule(e.g., RNA, DNA, protein) to form a labeled molecule. Theoligonucleotide tag can comprise a target specific region, uniqueidentifier region, universal primer binding region, detectable labelregion, or any combination thereof. In some instances, the attachment ofthe oligonucleotide tag to the molecule results in the formation of aunique junction comprising at least a portion of the oligonucleotide tagand at least a portion of the molecule. An expression level of a gene orgene product can be determined by detecting and/or quantifying at leasta portion of the labeled molecule (e.g., unique junction,oligonucleotide tag, molecule). The absolute quantity of a targetmolecule can also be determined by detecting the number of uniqueoligonucleotide tags of the labeled molecules and/or the number ofunique junctions in the labeled molecules.

Further disclosed herein are absolute PCR methods for amplifying and/orquantifying one or more molecules. A schematic of the absolute PCRprotocol is depicted in FIG. 14. As shown in Step 1 of FIG. 14, anoligonucleotide tag (1404) comprising a universal primer binding site(1401), unique identifier region (1402) and a target specific region(1403) is hybridized to a target molecule (1405). As shown in Step 2 ofFIG. 14, the oligonucleotide tag (1404) may act as a primer and a copyof the target molecule (1405) can be synthesized by primer extension bya polymerase (e.g., DNA polymerase) to produce an amplicon (1406). Theamplicon (1406) may comprise a universal primer binding site (1401),unique identifier region (1402) and a complement of target molecule(1411). As shown in Step 3 of FIG. 14, a reverse primer (1407) cananneal to the amplicon (1406). As shown in Step 4 of FIG. 14, theamplicon (1406) can act as a template for synthesizing second amplicon(1408). The second amplicon (1408) can comprise a copy of the targetmolecule (1411′) and a complement of the universal primer binding site(1401′) and a complement of the unique identifier region (1402′). Asshown in Step 5 of FIG. 14, the amplicons (1406, 1408) can act astemplates for subsequent amplification with a forward primer (1409)comprising the universal primer binding site and a reverse primer (1410)comprising a target specific sequence. Each subsequent ampliconcomprises the unique identifier region (1402). By incorporating theunique identifier region into each amplicon, the amplificationefficiency and/or amplification bias can be determined. In addition, thequantity of the target molecules can be determined by counting thenumber of different unique identifier regions that are associated witheach target molecule. The absolute PCR method can be used for subsequentanalysis of the target molecules (Step 6 of FIG. 14). For example, theamplicons produced by the absolute PCR method can be used to detectand/or quantify one or more target molecules. Unincorporatedoligonucleotide tags can be removed by purification of the amplicons.

I. Labeling of Molecules with Oligonucleotide Tags

A. Stochastic Labeling of Molecules

The methods disclosed herein comprise the attachment of oligonucleotidetags to molecules in a sample. In some instances, attachment of theoligonucleotide tags to the molecules comprises stochastic labeling ofthe molecules. Methods for stochastically labeling molecules can befound, for example, in U.S. Ser. Nos. 12/969,581 and 13/327,526.Generally, the stochastic labeling method comprises the randomattachment of a plurality of oligonucleotide tags to one or moremolecules. The plurality oligonucleotide tags are provided in excess ofthe one or more molecules to be labeled. In stochastic labeling, eachindividual molecule to be labeled has an individual probability ofattaching to the plurality of oligonucleotide tags. The probability ofeach individual molecule to be labeled attaching to a particular tag canbe about the same as any other individual molecule to be labeled.Accordingly, in some instances, the probability of any of the moleculesin a sample finding any of the tags is assumed to be equal, anassumption that can be used in mathematical calculations to estimate thenumber of molecules in the sample. In some circumstances the probabilityof attaching can be manipulated by, for example electing tags withdifferent properties that would increase or decrease the bindingefficiency of that tag with a individual molecule. The oligonucleotidetags can also be varied in numbers to alter the probability that aparticular tag will find a binding partner during the stochasticlabeling. For example one tag may be overrepresented in a pool of tags,thereby increasing the chances that the overrepresented tag finds atleast one binding partner.

B. Methods for Attaching an Oligonucleotide Tag to a Molecule

Attachment of an oligonucleotide tag to a molecule can occur by avariety of methods, including, but not limited to, hybridization of theoligonucleotide tag to the molecule. In some instances, theoligonucleotide tag comprises a target specific region. The targetspecific region can comprise a sequence that is complementary to atleast a portion of the molecule to be labeled. The target specificregion can hybridize to the molecule, thereby producing a labeledmolecule.

Attachment of the oligonucleotide tag to a molecule can occur byligation. Ligation techniques comprise blunt-end ligation and sticky-endligation. Ligation reactions can include DNA ligases such as DNA ligaseI, DNA ligase III, DNA ligase IV, and T4 DNA ligase. Ligation reactionscan include RNA ligases such as T4 RNA ligase I and T4 RNA ligase II.

Methods of ligation are described, for example in Sambrook et al. (2001)and the New England BioLabs catalog both of which are incorporatedherein by reference for all purposes. Methods include using T4 DNALigase which catalyzes the formation of a phosphodiester bond betweenjuxtaposed 5′ phosphate and 3′ hydroxyl termini in duplex DNA or RNAwith blunt and sticky ends; Taq DNA Ligase which catalyzes the formationof a phosphodiester bond between juxtaposed 5′ phosphate and 3′ hydroxyltermini of two adjacent oligonucleotides which are hybridized to acomplementary target DNA; E. coli DNA ligase which catalyzes theformation of a phosphodiester bond between juxtaposed 5′-phosphate and3′-hydroxyl termini in duplex DNA containing cohesive ends; and T4 RNAligase which catalyzes ligation of a 5′ phosphoryl-terminated nucleicacid donor to a 3′ hydroxyl-terminated nucleic acid acceptor through theformation of a 3′→5′ phosphodiester bond, substrates includesingle-stranded RNA and DNA as well as dinucleoside pyrophosphates; orany other methods described in the art. Fragmented DNA may be treatedwith one or more enzymes, for example, an endonuclease, prior toligation of adaptors to one or both ends to facilitate ligation bygenerating ends that are compatible with ligation.

In some instances, both ends of the oligonucleotide tag are attached tothe molecule. For example, both ends of the oligonucleotide tag can behybridized and/or ligated to one or more ends of the molecule. In someinstances, attachment of both ends of the oligonucleotide tag to bothends of the molecule results in the formation of a circularizedlabeled-molecule. Both ends of the oligonucleotide tag can also beattached to the same end of the molecule. For example, the 5′ end of theoligonucleotide tag is ligated to the 3′ end of the molecule and the 3′end of the oligonucleotide tag is hybridized to the 3′ end of themolecule, resulting in a labeled-molecule with a hairpin structure atone end. In some instances the oligonucleotide tag is attached to themiddle of the molecule.

In some instances, attachment of the oligonucleotide tag to the moleculecomprises the use of one or more adaptors. Adaptors can comprise atarget specific region on one end, which allows the attachment of theadaptor to the molecule, and an oligonucleotide tag specific region onthe other end, which allows attachment of the oligonucleotide tag to theadaptor. Adaptors can be attached to the molecule and/or oligonucleotideby methods including, but not limited to, hybridization and/or ligation.

Methods for ligating adaptors to fragments of nucleic acid are wellknown. Adaptors may be double-stranded, single-stranded or partiallysingle-stranded. In preferred aspects adaptors are formed from twooligonucleotides that have a region of complementarity, for example,about 10 to 30, or about 15 to 40 bases of perfect complementarity, sothat when the two oligonucleotides are hybridized together they form adouble stranded region. Optionally, either or both of theoligonucleotides may have a region that is not complementary to theother oligonucleotide and forms a single stranded overhang at one orboth ends of the adaptor. Single-stranded overhangs may preferably byabout 1 to about 8 bases, and most preferably about 2 to about 4. Theoverhang may be complementary to the overhang created by cleavage with arestriction enzyme to facilitate “sticky-end” ligation. Adaptors mayinclude other features, such as primer binding sites and restrictionsites. In some aspects the restriction site may be for a Type IISrestriction enzyme or another enzyme that cuts outside of itsrecognition sequence, such as EcoP151 (see, Mucke et al. J Mol Biol2001, 312(4):687-698 and U.S. Pat. No. 5,710,000 which is incorporatedherein by reference in its entirety).

The oligonucleotide tag can be attached to any region of a molecule. Forexample, the oligonucleotide can be attached to the 5′ or 3′ end of apolynucleotide (e.g., DNA, RNA). For example, the target-specific regionof the oligonucleotide tag comprises a sequence that is complementary toa sequence in the 5′ region of the molecule. The target-specific regionof the oligonucleotide tag can also comprise a sequence that iscomplementary to a sequence in the 3′ region of the molecule. In someinstances, the oligonucleotide tag is attached a region within a gene orgene product. For example, genomic DNA is fragmented and anoligonucleotide tag is attached to the fragmented DNA. In otherinstances, an RNA molecule is alternatively spliced and theoligonucleotide tag is attached to the alternatively spliced variants.In another example, the polynucleotide is digested and theoligonucleotide tag is attached to the digested polynucleotide. Inanother example, the target-specific region of the oligonucleotide tagcomprises a sequence that is complementary to a sequence within themolecule.

II. Reverse Transcription

In some instances, the methods disclosed herein comprise attachment ofan oligonucleotide tag to an RNA molecule to produce a labeled-RNAmolecule. The methods disclosed herein can further comprise reversetranscription of the labeled-RNA molecule to produce a labeled-cDNAmolecule. In some instances, at least a portion of the oligonucleotidetag acts as a primer for the reverse transcription reaction. Forexample, as shown in FIG. 1, Steps 1A-B, an oligonucleotide tagcomprising an oligodT sequence hybridizes to the polyA tail of an mRNAmolecule. The oligodT portion of the oligonucleotide tag acts as aprimer for first strand synthesis of the cDNA molecule.

In some instances the labeled cDNA molecule can be used as a moleculefor a new stochastic labeling reaction. The labeled cDNA can have afirst tag or set of tags from attachment to the RNA prior to reversetranscription and a second tag or set of tags attached to the cDNAmolecule. These multiple labeling reactions can, for example, be used todetermine the efficiency of events that occur between the attachment ofthe first and second tags, e.g. an optional amplification reaction orthe reverse transcription reaction.

In another example, an oligonucleotide tag is attached to the 5′ end ofan RNA molecule to produce a labeled-RNA molecule. Reverse transcriptionof the labeled-RNA molecule can occur by the addition of a reversetranscription primer. In some instances, the reverse transcriptionprimer is an oligodT primer, random hexanucleotide primer, or atarget-specific oligonucleotide primer. Generally, oligo(dT) primers are12-18 nucleotides in length and bind to the endogenous poly(A)+tail atthe 3′ end of mammalian mRNA. Random hexanucleotide primers can bind tomRNA at a variety of complementary sites. Target-specificoligonucleotide primers typically selectively prime the mRNA ofinterest.

In some instances, the method comprises repeatedly reverse transcribingthe labeled-RNA molecule to produce multiple labeled-cDNA molecules. Themethods disclosed herein can comprise conducting at least about 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 reversetranscription reactions. The method can comprise conducting at leastabout 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100reverse transcription reactions.

III. Amplification of Labeled Molecules

The methods disclosed herein may comprise amplification of the labeledmolecules to produce labeled amplicons. Amplification of the labeledmolecules can comprise PCR-based methods or non-PCR based methods.Amplification of the labeled molecules may comprise exponentialamplification of the labeled molecules. Amplification of the labeledmolecules may comprise linear amplification of the labeled molecules.

In some instances, amplification of the labeled molecules comprisesnon-PCR based methods. Examples of non-PCR based methods include, butare not limited to, multiple displacement amplification (MDA),transcription-mediated amplification (TMA), nucleic acid sequence-basedamplification (NASBA), strand displacement amplification (SDA),real-time SDA, rolling circle amplification, or circle-to-circleamplification.

Amplification of the labeled molecules may comprise hybridization chainreaction (HCR) based methods (Dirks and Pierce, PNAS, 2004; Zhang etal., Anal Chem, 2012). HCR based methods may comprise DNA-based HCR. HCRbased methods may comprise one or more labeled probes. The one or morelabeled probes may comprise one or more oligonucleotide tags disclosedherein.

In some instances, the methods disclosed herein further compriseconducting a polymerase chain reaction on the labeled-molecule (e.g.,labeled-RNA, labeled-DNA, labeled-cDNA) to produce a labeled-amplicon.The labeled-amplicon can be double-stranded molecule. Thedouble-stranded molecule can comprise a double-stranded RNA molecule, adouble-stranded DNA molecule, or a RNA molecule hybridized to a DNAmolecule. One or both of the strands of the double-stranded molecule cancomprise the oligonucleotide tag. Alternatively, the labeled-amplicon isa single-stranded molecule. The single-stranded molecule can compriseDNA, RNA, or a combination thereof. The nucleic acids of the presentinvention can comprise synthetic or altered nucleic acids.

The polymerase chain reaction can be performed by methods such as PCR,HD-PCR, Next Gen PCR, digital RTA, or any combination thereof.Additional PCR methods include, but are not limited to, allele-specificPCR, Alu PCR, assembly PCR, asymmetric PCR, droplet PCR, emulsion PCR,helicase dependent amplification HDA, hot start PCR, inverse PCR,linear-after-the-exponential (LATE)-PCR, long PCR, multiplex PCR, nestedPCR, hemi-nested PCR, quantitative PCR, RT-PCR, real time PCR, singlecell PCR, and touchdown PCR.

In some instances, conducting a polymerase chain reaction comprisesannealing a first target specific primer to the labeled-molecule.Alternatively or additionally, conducting a polymerase chain reactionfurther comprises annealing a universal primer to a universal primerbinding site region of the oligonucleotide tag, wherein theoligonucleotide tag is on a labeled-molecule or labeled-amplicon. Themethods disclosed herein can further comprise annealing a second targetspecific primer to the labeled-molecule and/or labeled-amplicon.

In some instances, the method comprises repeatedly amplifying thelabeled-molecule to produce multiple labeled-amplicons. The methodsdisclosed herein can comprise conducting at least about 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amplificationreactions. Alternatively, the method comprises conducting at least about25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100amplification reactions.

Other suitable amplification methods include the ligase chain reaction(LCR) (for example, Wu and Wallace, Genomics 4, 560 (1989), Landegren etal., Science 241, 1077 (1988) and Barringer et al. Gene 89:117 (1990)),transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA 86,1173 (1989) and WO88/10315), self-sustained sequence replication(Guatelli et al., Proc. Nat. Acad. Sci. USA, 87, 1874 (1990) andWO90/06995), selective amplification of target polynucleotide sequences(U.S. Pat. No. 6,410,276), consensus sequence primed polymerase chainreaction (CP-PCR) (U.S. Pat. No. 4,437,975), arbitrarily primedpolymerase chain reaction (AP-PCR) (U.S. Pat. Nos. 5,413,909,5,861,245), rolling circle amplification (RCA) (for example, Fire andXu, PNAS 92:4641 (1995) and Liu et al., J. Am. Chem. Soc. 118:1587(1996)) and U.S. Pat. No. 5,648,245, strand displacement amplification(see Lasken and Egholm, Trends Biotechnol. 2003 21(12):531-5; Barker etal. Genome Res. 2004 May; 14(5):901-7; Dean et al. Proc Natl Acad SciUSA. 2002; 99(8):5261-6; Walker et al. 1992, Nucleic Acids Res.20(7):1691-6, 1992 and Paez, et al. Nucleic Acids Res. 2004; 32(9):e71),Qbeta Replicase, described in PCT Patent Application No. PCT/US87/00880and nucleic acid based sequence amplification (NABSA). (See, U.S. Pat.Nos. 5,409,818, 5,554,517, and 6,063,603, each of which is incorporatedherein by reference), Other amplification methods that may be used aredescribed in, U.S. Pat. Nos. 6,582,938, 5,242,794, 5,494,810, 4,988,617,and US Pub. No. 20030143599 each of which is incorporated herein byreference. DNA may also be amplified by multiplex locus-specific PCR orusing adaptor-ligation and single primer PCR (See Kinzler andVogelstein, NAR (1989) 17:3645-53. Other available methods ofamplification, such as balanced PCR (Makrigiorgos, et al. (2002), NatBiotechnol, Vol. 20, pp. 936-9), may also be used.

Molecular inversion probes (“MIPs”) may also be used for amplificationof selected targets. MIPs may be generated so that the ends of thepre-circle probe are complementary to regions that flank the region tobe amplified. The gap can be closed by extension of the end of the probeso that the complement of the target is incorporated into the MIP priorto ligation of the ends to form a closed circle. The closed circle canbe amplified and detected by sequencing or hybridization as previouslydisclosed in Hardenbol et al., Genome Res. 15:269-275 (2005) and in U.S.Pat. No. 6,858,412.

Amplification of the labeled molecule may comprise the use of one ormore primers. FIG. 9 shows an exemplary forward and reverse primers. Theforward primer (901) may comprise a universal PCR sequence (902), uniqueidentifier sequence (903) and target sequence (904). The reverse primer(905) may comprise a target sequence.

Primers used in the method can be designed with the use of the Primer 3,a computer program which suggests primer sequences based on a userdefined input sequence. Other primer designs may also be used, orprimers may be selected by eye without the aid of computer programs.There are many options available with the program to tailor the primerdesign to most applications. Primer 3 can consider many factors,including, but not limited to, oligo melting temperature, length, GCcontent, 3′ stability, estimated secondary structure, the likelihood ofannealing to or amplifying undesirable sequences (for exampleinterspersed repeats) and the likelihood of primer-dimer formationbetween two copies of the same primer. In the design of primer pairs,Primer 3 can consider product size and melting temperature, thelikelihood of primer-dimer formation between the two primers in thepair, the difference between primer melting temperatures, and primerlocation relative to particular regions of interest to be avoided.

IV. Sequencing

In some aspects, the methods disclosed herein further comprisedetermining the sequence of the labeled-molecule or any product thereof(e.g., labeled-amplicons, labeled-cDNA molecules). Determining thesequence of the labeled-molecule or any product thereof can compriseconducting a sequencing reaction to determine the sequence of at least aportion of the oligonucleotide tag, at least a portion of thelabeled-cDNA molecule, a complement thereof, a reverse complementthereof, or any combination thereof. In some instances only the tag or aportion of the tag is sequenced. Determining the sequence of thelabeled-molecule or any product thereof can be performed by sequencingmethods such as Helioscope™ single molecule sequencing, Nanopore DNAsequencing, Lynx Therapeutics' Massively Parallel Signature Sequencing(MPSS), 454 pyrosequencing, Single Molecule real time (RNAP) sequencing,Illumina (Solexa) sequencing, SOLiD sequencing, Ion Torrent™, Ionsemiconductor sequencing, Single Molecule SMRT™ sequencing, Polonysequencing, DNA nanoball sequencing, and VisiGen Biotechnologiesapproach. Alternatively, determining the sequence of thelabeled-molecule or any product thereof can use sequencing platforms,including, but not limited to, Genome Analyzer IIx, HiSeq, and MiSeqoffered by Illumina, Single Molecule Real Time (SMRT™) technology, suchas the PacBio RS system offered by Pacific Biosciences (California) andthe Solexa Sequencer, True Single Molecule Sequencing (tSMS™) technologysuch as the HeliScope™ Sequencer offered by Helicos Inc. (Cambridge,Mass.).

In some instances, determining the sequence of the labeled-molecule orany product thereof comprises paired-end sequencing, nanoporesequencing, high-throughput sequencing, shotgun sequencing,dye-terminator sequencing, multiple-primer DNA sequencing, primerwalking, Sanger dideoxy sequencing, Maxim-Gilbert sequencing,pyrosequencing, true single molecule sequencing, or any combinationthereof. Alternatively, the sequence of the labeled-molecule or anyproduct thereof can be determined by electron microscopy or achemical-sensitive field effect transistor (chemFET) array.

In another example, determining the sequence of labeled-molecules or anyproduct thereof comprises RNA-Seq or microRNA sequencing. Alternatively,determining the sequence of labeled-molecules or any products thereofcomprises protein sequencing techniques such as Edman degradation,peptide mass fingerprinting, mass spectrometry, or protease digestion.

The sequencing reaction can, in certain embodiments, occur on a solid orsemi-solid support, in a gel, in an emulsion, on a surface, on a bead,in a drop, in a continuous follow, in a dilution, or in one or morephysically separate volumes.

Sequencing may comprise sequencing at least about 10, 20, 30, 40, 50,60, 70, 80, 90, 100 or more nucleotides or base pairs of the labeledmolecule. In some instances, sequencing comprises sequencing at leastabout 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more nucleotidesor base pairs of the labeled molecule. In other instances, sequencingcomprises sequencing at least about 1500; 2,000; 3,000; 4,000; 5,000;6,000; 7,000; 8,000; 9,000; or 10,000 or more nucleotides or base pairsof the labeled molecule.

Sequencing may comprise at least about 200, 300, 400, 500, 600, 700,800, 900, 1000 or more sequencing reads per run. In some instances,sequencing comprises sequencing at least about 1500; 2,000; 3,000;4,000; 5,000; 6,000; 7,000; 8,000; 9,000; or 10,000 or more sequencingreads per run.

V. Detection Methods

The methods disclosed herein can further comprise detection of thelabeled-molecules and/or labeled-amplicons. Detection of thelabeled-molecules and/or labeled-amplicons can comprise hybridization ofthe labeled-molecules to surface, e.g. a solid support. Alternatively,or additionally, detection of the labeled-molecules comprises contactingthe labeled-molecules and/or labeled-amplicons with surface, e.g. asolid support. In some instances, the method further comprisescontacting the labeled-molecules and/or labeled-amplicons with adetectable label to produce a detectable-label conjugatedlabeled-molecule. The methods disclosed herein can further comprisedetecting the detectable-label conjugated labeled-molecule. Detection ofthe labeled-molecules or any products thereof (e.g., labeled-amplicons,detectable-label conjugated labeled-molecule) can comprise detection ofat least a portion of the oligonucleotide tag, molecule, detectablelabel, a complement of the oligonucleotide tag, a complement of themolecule, or any combination thereof.

Detection of the labeled-molecules or any products thereof can comprisean emulsion. For example, the labeled-molecules or any products thereofcan be in an emulsion. Alternatively, detection of the labeled-moleculesor any products thereof comprises one or more solutions. In otherinstances, detection of the labeled-molecules comprises one or morecontainers.

Detection of the labeled-molecules or any products thereof (e.g.,labeled-amplicons, detectable-label conjugated labeled-molecule) cancomprise detecting each labeled-molecule or products thereof. Forexample, the methods disclosed herein comprise sequencing at least aportion of each labeled-molecule, thereby detecting eachlabeled-molecule.

In some instances, detection of the labeled-molecules and/orlabeled-amplicons comprises electrophoresis, spectroscopy, microscopy,chemiluminescence, luminescence, fluorescence, immunofluorescence,colorimetry, or electrochemiluminescence methods. For example, themethod comprises detection of a fluorescent dye. Detection of thelabeled-molecule or any products thereof can comprise colorimetricmethods. For example, the colorimetric method comprises the use of acolorimeter or a colorimetric reader. A non-limiting list ofcolorimeters and colorimetric readers include Sensovation's ColorimetricArray Imaging Reader (CLAIR), ESEQuant Lateral Flow Immunoassay Reader,SpectraMax 340PC 38, SpectraMax Plus 384, SpectraMax 190, VersaMax,VMax, and EMax.

Additional methods used alone or in combination with other methods todetect the labeled-molecules and/or amplicons can comprise the use of anarray detector, fluorescence reader, non-fluorescent detector, CRreader, luminometer, or scanner. In some instances, detecting thelabeled-molecules and/or labeled-amplicons comprises the use of an arraydetector. Examples of array detectors include, but are not limited to,diode-array detectors, photodiode array detectors, HLPC photodiode arraydetectors, pixel array detectors, Germanium array detectors, CMOS andCCD array detectors, Gated linear CCD array detectors, InGaAs photodiodearray systems, and TE cooled CCD systems. The array detector can be amicroarray detector. Non-limiting examples of microarray detectorsinclude microelectrode array detectors, optical DNA microarray detectionplatforms, DNA microarray detectors, RNA microarray detectors, andprotein microarray detectors.

In some instances, a fluorescence reader is used to detect thelabeled-molecule and/or labeled-amplicons. The fluorescence reader canread 1, 2, 3, 4, 5, or more color fluorescence microarrays or otherstructures on biochips, on slides, or in microplates. In some instances,the fluorescence reader is a Sensovation Fluorescence Array imagingReader (FLAIR). Alternatively, the fluorescence reader is a fluorescencemicroplate reader such as the Gemini XPS Fluorescence microplate reader,Gemini EM Fluorescence microplate reader, Finstruments® Fluoroskanfilter based fluorescence microplate reader, PHERAstar microplatereader, FlUOstar microplate reader, POLARstar Omega microplate reader,FLUOstar OPTIMA multi-mode microplate reader and POLARstar OPTIMAmulti-mode microplate reader. Additional examples of fluorescencereaders include PharosFX™ and PharosFX Plus systems.

In some instances, detection of the labeled-molecule and/orlabeled-amplicon comprises the use of a microplate reader. In someinstances, the microplate reader is an xMark™ microplate absorbancespectrophotometer, iMark microplate absorbance reader, EnSpire®Multimode plate reader, EnVision Multilabel plate reader, VICTOR XMultilabel plate reader, FlexStation, SpectraMax Paradigm, SpectraMaxM5e, SpectraMax M5, SpectraMax M4, SpectraMax M3, SpectraMax M2-M2e,FilterMax F series, Fluoroskan Ascent FL Microplate Fluoremeter andLuminometer, Fluoroskan Ascent Microplate Fluoremeter, Luminoskan AscentMicroplate Luminometer, Multiskan EX Microplate Photometer, Muliskan FCMicroplate Photometer, and Muliskan GO Microplate Photometer. In someinstances, the microplate reader detects absorbance, fluorescence,luminescence, time-resolved fluorescence, light scattering, or anycombination thereof. In some embodiments, the microplate reader detectsdynamic light scattering. The microplate reader, can in some instances,detect static light scattering. In some instances, detection of thelabeled-molecules and/or labeled-amplicons comprises the use of amicroplate imager. In some instances, the microplate imager comprisesViewLux uHTS microplate imager and BioRad microplate imaging system.

Detection of labeled-molecules and/or products thereof can comprise theuse of a luminometer. Examples of luminometers include, but are notlimited to, SpectraMax L, GloMax®-96 microplate luminometer,GloMax®-20/20 single-tube luminometer, GloMax®-Multi⁺ with Instinct™software, GloMax®-Multi Jr single tube multimode reader, LUMIstarOPTIMA, LEADER HC⁺ luminometer, LEADER450i luminometer, and LEADER50iluminometer.

In some instances, detection of the labeled-molecules and/orlabeled-amplicons comprises the use of a scanner. Scanners includeflatbed scanners such as those provided by Cannon, Epson, HP, Fujitsu,and Xerox. Additional examples of flatbed scanners include the FMBIO®fluorescence imaging scanners (e.g., FMBIO® II, III, and III Plussystems). Scanners can include microplate scanners such as the ArrayitArrayPix™ microarray microplate scanner. In some instances, the scanneris a Personal Molecular Imager™ (PMI) system provided by Bio-rad.

Detection of the labeled-molecule can comprise the use of an analyticaltechnique that measures the mass-to-charge ratio of charged particles,e.g. mass spectrometry. In some embodiments the mass-to-charge ratio ofcharged particles is measured in combination with chromatographicseparation techniques. In some embodiments sequencing reactions are usedin combination with mass-to-charge ratio of charged particlemeasurements. In some embodiments the tags comprise isotopes. In someembodiments the isotope type or ratio is controlled or manipulated inthe tag library.

Detection of the labeled-molecule or any products thereof comprises theuse of small particles and/or light scattering. For example, theamplified molecules (e.g., labeled-amplicons) are attached to haptens ordirectly to small particles and hybridized to the array. The smallparticles can be in the nanometer to micrometer range in size. Theparticles can be detected when light is scattered off of its surface.

A colorimetric assay can be used where the small particles are colored,or haptens can be stained with colorimetric detection systems. In someinstances, a flatbed scanner can be used to detect the light scatteredfrom particles, or the development of colored materials. The methodsdisclosed herein can further comprise the use of a light absorbingmaterial. The light absorbing material can be used to block undesirablelight scatter or reflection. The light absorbing material can be a foodcoloring or other material. In some instances, detection of thelabeled-molecule or any products thereof comprises contacting thelabeled-molecule with an off-axis white light.

Detection of the labeled-molecule may comprise hybridization chainreaction (HCR). As depicted in FIG. 33, a sample comprising a pluralityof nucleic acid molecules (3340) is stochastically labeled with aplurality of oligonucleotide tags (3330). The oligonucleotide tags(3330) comprise a unique identifier region (3310) and an adapter region(3320). Stochastically labeling the nucleic acid molecules can compriseattachment of one or more oligonucleotide tags (3330) to one or moreends of the nucleic acid molecule (3340) to produce one or morelabeled-molecules (3345). The one or more labeled molecules can becontacted with a plurality of HCR probes (3350). The plurality of HCRprobes (3350) may comprise a hairpin molecules with an overhang and oneor more labels (3360, 3390). The plurality of HCR probes (3350) maycomprise a mixture of hairpin molecules with 5′ overhangs and hairpinmolecules with 3′ overhangs. The plurality of HCR probes may comprise astem (3370, 3380). The sequence of the stem (3370, 3380) may becomplementary to at least a portion of the oligonucleotide tag. Thesequence of the stem (3370, 3380) may be complementary to the adapterregion (3320) of the oligonucleotide tag. The adapter region (3320) ofthe oligonucleotide may act as an initiator for a hybridization chainreaction. As shown in FIG. 33, the stem (3370) of the HCR probe (3350)can hybridize to the adapter region (3320) of the labeled molecule(3345). Hybridization of the stem (3370) of the HCR probe (3350) to theadapter region (3320) of the labeled molecule (3345) can result inopening of the stem (e.g., 3370 and 3380 of the stem are no longerannealed) and linearization of the HCR probe (3350), which results inthe formation of a labeled molecule hybridized to a HCR probe (3355).The linearized HCR probe can then act as an initiator for subsequenthybridization of another HCR probe. The stem of a second HCR probe canhybridize to the linearized HCR probe that has hybridized to the labeledmolecule, resulting in linearization of the second HCR probe and theformation of a labeled-molecule containing two linearized HCR probes.The linearized second HCR probe can act as an initiator for anotherhybridization reaction. This process can be repeated multiple times toproduce a labeled molecule with multiple linearized HCR probes (3375).The labels (3360, 3390) on the HCR probe can enable detection of thelabeled molecule. The labels (3360, 3390) may be any type of label(e.g., fluorophore, chromophore, small molecule, nanoparticle, hapten,enzyme, antibody, magnet). The labels (3360 and 3390) may comprisefragments of a single label. The labels (3360, 3390) may generate adetectable signal when they are in close proximity. When the HCR probeis a hairpin, the labels (3360 and 3390) may be too far away to producea detectable signal. When the HCR probe is linearized and multiplelinearized HCR probes are hybridized together, the labels (3360, 3390)may be in close enough proximity to generate a detectable signal. Forexample, a HCR probe (3350) may comprise two pyrene moieties as labels(3360, 3390). Alternatively, the labels may be nanoparticles. The HCRcan enable attachment of multiple HCR probes to a labeled molecule,which can result in signal amplification. Stochastic labeling followedby HCR may increase the sensitivity of detection, analysis and/orquantification of the nucleic acid molecules. Stochastic labelingfollowed by HCR may increase the accuracy of detection, analysis, and/orquantification of one or more nucleic acid molecules.

Additional methods and apparatus for signal detection and processing ofintensity data are disclosed in, for example, U.S. Pat. Nos. 5,143,854,5,547,839, 5,578,832, 5,631,734, 5,800,992, 5,834,758, 5,856,092,5,902,723, 5,936,324, 5,981,956, 6,025,601, 6,090,555, 6,141,096,6,185,030, 6,201,639; 6,218,803; and 6,225,625, in U.S. Patent Pub. Nos.20040012676 and 20050059062 and in PCT Application PCT/US99/06097(published as WO99/47964), each of which also is hereby incorporated byreference in its entirety for all purposes.

Detection and/or quantification of the labeled molecules may comprisethe use of computers or computer software. Computer software productsmay comprise a computer readable medium having computer-executableinstructions for performing the logic steps of the method of theinvention. Suitable computer readable medium include floppy disk,CD-ROM/DVD/DVD-ROM, hard-disk drive, flash memory, ROM/RAM, magnetictapes, etc. The computer-executable instructions may be written in asuitable computer language or combination of several languages. Basiccomputational biology methods are described in, for example, Setubal andMeidanis et al., Introduction to Computational Biology Methods (PWSPublishing Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.),Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998);Rashidi and Buehler, Bioinformatics Basics: Application in BiologicalScience and Medicine (CRC Press, London, 2000) and Ouelette and BzevanisBioinformatics: A Practical Guide for Analysis of Gene and Proteins(Wiley & Sons, Inc., 2^(nd) ed., 2001). See also U.S. Pat. No.6,420,108.

Computer program products and software may be used for a variety ofpurposes, such as probe design, management of data, analysis, andinstrument operation. See, U.S. Pat. Nos. 5,593,839, 5,795,716,5,733,729, 5,974,164, 6,066,454, 6,090,555, 6,185,561, 6,188,783,6,223,127, 6,229,911 and 6,308,170. Computer methods related togenotyping using high density microarray analysis may also be used inthe present methods, see, for example, US Patent Pub. Nos. 20050250151,20050244883, 20050108197, 20050079536 and 20050042654. Additionally, thepresent disclosure may have preferred embodiments that include methodsfor providing genetic information over networks such as the Internet asshown in U.S. Patent Pub. Nos. 20030097222, 20020183936, 20030100995,20030120432, 20040002818, 20040126840, and 20040049354.

Detection and/or quantification of the labeled-molecules or any productsthereof can comprise the use of one or more algorithms. Alternatively,or additionally, the methods, kits and compositions can further comprisea computer, software, printer, and/or electronic data or information.

The methods disclosed herein can further comprise the transmission ofdata/information. For example, data/information derived from thedetection and/or quantification of the labeled-molecule or any productsthereof are transmitted to another device and/or instrument. In someinstances, the information obtained from an algorithm can also betransmitted to another device and/or instrument. Transmission of thedata/information can comprise the transfer of data/information from afirst source to a second source. The first and second sources can be inthe same approximate location (e.g., within the same room, building,block, campus). Alternatively, first and second sources are in multiplelocations (e.g., multiple cities, states, countries, continents, etc).In some embodiments a non-transitory computable readable media is usedto store or analyze data generated using methods described herein.

Transmission of the data/information can comprise digital transmissionor analog transmission. Digital transmission can comprise the physicaltransfer of data (a digital bit stream) over a point-to-point orpoint-to-multipoint communication channel. Examples of such channels arecopper wires, optical fibres, wireless communication channels, andstorage media. The data can be represented as an electromagnetic signal,such as an electrical voltage, radiowave, microwave, or infrared signal.

Analog transmission can comprise the transfer of a continuously varyinganalog signal. The messages can either be represented by a sequence ofpulses by means of a line code (baseband transmission), or by a limitedset of continuously varying wave forms (passband transmission), using adigital modulation method. The passband modulation and correspondingdemodulation (also known as detection) can be carried out by modemequipment. According to the most common definition of digital signal,both baseband and passband signals representing bit-streams areconsidered as digital transmission, while an alternative definition onlyconsiders the baseband signal as digital, and passband transmission ofdigital data as a form of digital-to-analog conversion.

The applications and uses of the systems and methods described hereincan produce one or more result useful to diagnose a disease state of anindividual, for example, a patient. In one embodiment, a method ofdiagnosing a disease comprises reviewing or analyzing data relating tothe presence and/or the concentration level of a target in a sample. Aconclusion based review or analysis of the data can be provided to apatient, a health care provider or a health care manager. In oneembodiment the conclusion is based on the review or analysis of dataregarding a disease diagnosis. It is envisioned that in anotherembodiment that providing a conclusion to a patient, a health careprovider or a health care manager includes transmission of the data overa network.

Accordingly, business systems and methods using the systems and methodsdescribed herein are provided.

One aspect of the invention is a business method comprising screeningpatient test samples for the presence or absence of a biologicallyactive analyte to produce data regarding the analyte, collecting theanalyte data, providing the analyte data to a patient, a health careprovider or a health care manager for making a conclusion based onreview or analysis of the data regarding a disease diagnosis. In oneembodiment the conclusion is provided to a patient, a health careprovider or a health care manager includes transmission of the data overa network.

Accordingly FIG. 8 is a block diagram showing a representative examplelogic device through which reviewing or analyzing data relating to thepresent invention can be achieved. Such data can be in relation to adisease, disorder or condition in an individual. FIG. 8 shows a computersystem (or digital device) 800 connected to an apparatus 820 for usewith the scanning sensing system 824 to, for example, produce a result.The computer system 800 may be understood as a logical apparatus thatcan read instructions from media 811 and/or network port 805, which canoptionally be connected to server 809 having fixed media 812. The systemshown in FIG. 8 includes CPU 801, disk drives 803, optional inputdevices such as keyboard 815 and/or mouse 816 and optional monitor 807.Data communication can be achieved through the indicated communicationmedium to a server 809 at a local or a remote location. Thecommunication medium can include any means of transmitting and/orreceiving data. The communication medium can comprise a non-transitorycomputer readable media. For example, the communication medium can be anetwork connection, a wireless connection or an internet connection.Such a connection can provide for communication over the World Wide Web.It is envisioned that data can be transmitted over such networks orconnections for reception and/or review by a party 822. The receivingparty 822 can be but is not limited to a patient, a health care provideror a health care manager.

In one embodiment, a computer-readable medium includes a medium suitablefor transmission of a result of an analysis of an environmental orbiological sample. The medium can include a result regarding a diseasecondition or state of a subject, wherein such a result is derived usingthe methods described herein. The computer readable media can benon-transitory.

Data Analysis: In some embodiments the scanner instrument produces theraw intensity values for each position on the array as well as thebackground intensity. Many methods can be used to calculate the numberof molecules in the sample. For example, the values for the controlpositions on the array are removed from the dataset and a scatter plotis generated to provide an image of the data. This may occur with orwithout the background intensity subtracted from the raw data. Athreshold intensity value can be established in order to classify thepositive spots and the negative spots. All of the positive spots aresummed to provide a total count of unique stochastic labels. Thisprocess can be automated in Microsoft excel or another computer softwareprogram.

An alternative to this strategy is the use of clustering algorithms suchas k-means clustering. K-means clustering is a method of clusteranalysis which aims to partition all of the observations into clustersin which each observation belongs to the cluster with the nearest mean.The data can be split into 2 or 3 clusters (or more, 3 clusters seems toproduce the cleanest numbers so far) and the number of data points canbe added up to determine the counts.

VI. Target Molecules

The methods, kits, and systems disclosed herein can be used in thestochastic labeling of molecules. Such molecules include, but are notlimited to, polynucleotides and polypeptides. As used herein, the terms“polynucleotide” and “nucleic acid molecule” refers to a polymeric formof nucleotides of any length, either ribonucleotides,deoxyribonucleotides, locked nucleic acids (LNA) or peptide nucleicacids (PNAs), that comprise purine and pyrimidine bases, or othernatural, chemically or biochemically modified, non-natural, orderivatized nucleotide bases. A “polynucleotide” or “nucleic acidmolecule” can consist of a single nucleotide or base pair.Alternatively, the “polynucleotide” or “nucleic acid molecule” comprisestwo or more nucleotides or base pairs. For example, the “polynucleotide”or “nucleic acid molecule” comprises at least about 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80,90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides orbase pairs. In another example, the polynucleotide comprises at leastabout 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500,7000, 7500, 8000, 8500, 9000, 9500, or 10000 nucleotides or base pairs.The backbone of the polynucleotide can comprise sugars and phosphategroups, as may typically be found in RNA or DNA, or modified orsubstituted sugar or phosphate groups. A polynucleotide may comprisemodified nucleotides, such as methylated nucleotides and nucleotideanalogs. The sequence of nucleotides may be interrupted bynon-nucleotide components. Thus the terms nucleoside, nucleotide,deoxynucleoside and deoxynucleotide generally include analogs such asthose described herein. These analogs are those molecules having somestructural features in common with a naturally occurring nucleoside ornucleotide such that when incorporated into a nucleic acid oroligonucleoside sequence, they allow hybridization with a naturallyoccurring nucleic acid sequence in solution. Typically, these analogsare derived from naturally occurring nucleosides and nucleotides byreplacing and/or modifying the base, the ribose or the phosphodiestermoiety. The changes can be tailor made to stabilize or destabilizehybrid formation or enhance the specificity of hybridization with acomplementary nucleic acid sequence as desired. In some instances, themolecules are DNA, RNA, or DNA-RNA hybrids. The molecules can besingle-stranded or double-stranded. In some instances, the molecules areRNA molecules, such as mRNA, rRNA, tRNA, ncRNA, lncRNA, siRNA, or miRNA.The RNA molecules can be polyadenylated. Alternatively, the mRNAmolecules are not polyadenylated. Alternatively, the molecules are DNAmolecules. The DNA molecules can be genomic DNA. The DNA molecules cancomprise exons, introns, untranslated regions, or any combinationthereof.

In some instances, the molecules are polypeptides. As used herein, theterm “polypeptide” refers to a molecule comprising at least one peptide.In some instances, the polypeptide consists of a single peptide.Alternatively, the polypeptide comprises two or more peptides. Forexample, the polypeptide comprises at least about 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80,90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 peptides.Examples of polypeptides include, but are not limited to, amino acids,proteins, peptides, hormones, oligosaccharides, lipids, glycolipids,phospholipids, antibodies, enzymes, kinases, receptors, transcriptionfactors, and ligands.

The methods, kits, and systems disclosed herein can be used tostochastically label individual occurrences of identical or nearlyidentical molecules and/or different molecules. In some instances, themethods, kits, and systems disclosed herein can be used tostochastically label identical or nearly identical molecules (e.g.,molecules comprise identical or nearly identical sequences). Forexample, the molecules to be labeled comprise at least about 80%, 85%,90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity. The nearlyidentical molecules may differ by less than about 100, 90, 80, 70, 60,50, 40, 30, 25, 20, 25, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotides orbase pairs. In some instances, the molecules to be labeled are variantsof each other. For example, the molecules to be labeled may containsingle nucleotide polymorphisms or other types of mutations. In anotherexample, the molecules to be labeled are splice variants. In someinstances, at least one molecule is stochastically labeled. In otherinstances, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 identical or nearlyidentical molecules are stochastically labeled. Alternatively, at least20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800,900, or 1000 identical or nearly identical molecules are stochasticallylabeled. In other instances, at least 1500; 2,000; 2500; 3,000; 3500;4,000; 4500; 5,000; 6,000; 7,000; 8,000; 9,000; or 10000 identical ornearly identical molecules are stochastically labeled. In otherinstances; at least 15,000; 20,000; 25,000; 30,000; 35,000; 40,000;45,000; 50,000; 60,000; 70,000; 80,000; 90,000; or 100,000 identical ornearly identical molecules are stochastically labeled.

In other instances, the methods, kits, and systems disclosed herein canbe used to stochastically label different molecules. For example, themolecules to be labeled comprise less than 75%, 70%, 65%, 60%, 55%, 50%,45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1% sequenceidentity. The different molecules may differ by at least about 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 ormore nucleotides or base pairs. In some instances, at least one moleculeis stochastically labeled. In other instances, at least 2, 3, 4, 5, 6,7, 8, 9, or 10 different molecules are stochastically labeled.Alternatively, at least 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300,400, 500, 600, 700, 800, 900, or 1000 different molecules arestochastically labeled. In other instances, at least 1500; 2,000; 2500;3,000; 3500; 4,000; 4500; 5,000; 6,000; 7,000; 8,000; 9,000; or 10000different molecules are stochastically labeled. In other instances; atleast 15,000; 20,000; 25,000; 30,000; 35,000; 40,000; 45,000; 50,000;60,000; 70,000; 80,000; 90,000; or 100,000 different molecules arestochastically labeled.

The different molecules to be labeled can be present in the sample atdifferent concentrations or amounts. For example, the concentration oramount of one molecule is greater than the concentration or amount ofanother molecule in the sample. In some instances, the concentration oramount of at least one molecule in the sample is at least about 1.5, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50,60, 70, 80, 90, or 100 or more times greater than the concentration oramount of at least one other molecule in the sample. In another example,the concentration or amount of one molecule is less than theconcentration or amount of another molecule in the sample. Theconcentration or amount of at least one molecule in the sample can be atleast about 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25,30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 or more times less than theconcentration or amount of at least one other molecule in the sample.

In some instances, the molecules to be labeled are in one or moresamples. The molecules to be labeled can be in two or more samples. Thetwo or more samples can contain different amounts or concentrations ofthe molecules to be labeled. In some instances, the concentration oramount of one molecule in one sample can be greater than theconcentration or amount of the same molecule in a different sample. Forexample, a blood sample might contain a higher amount of a particularmolecule than a urine sample. Alternatively, a single sample is dividedinto two or more subsamples. The subsamples can contain differentamounts or concentrations of the same molecule. The concentration oramount of at least one molecule in one sample can be at least about 1.5,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45,50, 60, 70, 80, 90, or 100 or more times greater than the concentrationor amount of the same molecule in another sample. Alternatively, theconcentration or amount of one molecule in one sample can be less thanthe concentration or amount of the same molecule in a different sample.For example, a heart tissue sample might contain a higher amount of aparticular molecule than a lung tissue sample. The concentration oramount of at least one molecule in one sample can be at least about 1.5,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45,50, 60, 70, 80, 90, or 100 or more times less than the concentration oramount of the same molecule in another sample. In some instances, thedifferent concentrations or amounts of a molecule in two or moredifferent samples is referred to as sample bias.

VII. Oligonucleotide Tags

In some embodiments, the methods, kits, and systems disclosed hereincomprise a plurality of oligonucleotide tags. The oligonucleotide tagscan comprise a target specific region, a unique identifier region, anadapter region, a universal primer binding site region, or anycombination thereof. FIG. 10-13 shows exemplary oligonucleotide tags.

As shown in FIG. 10, the oligonucleotide tag (1004) may comprise auniversal primer binding site (1001), unique identifier region (1002)and a target specific region (1003).

As shown in FIG. 11A, the oligonucleotide tag (1107) can comprise auniversal primer binding site (1102), a unique identifier region (1103)and a target specific region (1105). The universal primer binding site(1102) may comprise a phosphorothioate linkage, as depicted by an “*” inFIG. 11A. As shown in FIG. 11B, the oligonucleotide tag (1128) cancomprise a universal primer binding site (1122), a unique identifierregion (1123), bridge splint (1129), and a target specific region(1126). As shown in FIG. 11C, the oligonucleotide tag (1158) maycomprise a universal primer binding site (1151), unique identifierregion (1152), ligation sequence (1153), and a target specific sequence(1157). As shown in FIG. 11D, the oligonucleotide tag (1177) maycomprise a universal primer binding site (1171), unique identifierregion (1172), ligation sequence (1173), and a DNA target specificsequence (1178).

As shown in FIG. 12A, an oligonucleotide tag (1201) may comprise auniversal primer binding site (1202), a unique identifier regioncomprising a degenerate sequence (1203) and a target specific region(1204). As shown in FIG. 12B, an oligonucleotide tag (1210) may comprisea universal primer binding site (1211), a unique identifier region(1215) comprising a degenerate sequence (1213) flanked by two flankingsequences (1212 and 1214) and a target specific region (1216).

The oligonucleotide tag may be comprise one or more secondarystructures. As shown in FIG. 13A, the oligonucleotide tag (1301)comprises a hairpin structure. The oligonucleotide tag (1301) cancomprise a target specific region (1302), a cleavable stem (1303, 1304),and a unique identifier region (1305).

The oligonucleotide tag may comprise a target specific region that canhybridize to a plurality of different target molecules. For example, asshown in FIG. 13B, the oligonucleotide tag (1310) comprises a universalprimer binding site (1311), unique identifier region (1312), and auniversal target specific region (1313). The universal target specificregion (1313) may comprise an oligodT sequence that enableshybridization to target molecules comprising a polyA or polyU sequence.

A method for synthesizing a plurality of oligonucleotide tags isdepicted in FIG. 10. As shown in FIG. 10, oligonucleotide tags (1004)can be synthesized separately. The oligonucleotide tags (1004) cancomprise a universal primer binding site (1001), a unique identifierregion (1002), and a target specific region. The individualoligonucleotide tags can be pooled to produce a plurality ofoligonucleotide tags (1005) comprising a plurality of different uniqueidentifier regions.

A method for synthesizing a plurality of oligonucleotide tags isdepicted in FIG. 11A. As shown in FIG. 11A, oligonucleotide fragments(1101) can be synthesized separately. The oligonucleotide fragments(1101) can comprise a universal primer binding site (1102) and a uniqueidentifier region (1103). The universal primer binding site (1102) maycomprise a phosphorothioate linkage, as depicted by an “*” in FIG. 11A.As shown in Step 1 of FIG. 11A, the individual oligonucleotide fragments(1101) may be mixed to produce a plurality of oligonucleotide fragments(1104). The plurality of oligonucleotide fragments (1104) can beattached to a target specific region (1105). As shown in Step 2 of FIG.11A, the target specific region can be ligated to the oligonucleotidetag to produce an oligonucleotide tag comprising a target specificregion (1105). 5′ and 3′ exonucleases may be added to the reaction toremove non-ligated products (1105, 1101). The oligonucleotide tag (1106)comprising the universal primer binding site (1102), unique identifierregion (1103) and target specific region (1105) may be resistant to 5′and 3′ exonucleases. As shown in Step 3 of FIG. 11A, the 3′ phosphategroup from the ligated oligonucleotide tag (1106) can be removed toproduce an oligonucleotide tag (1107) without a 3′ phosphate group. The3′ phosphate group can be removed enzymatically. For example, a T4polynucleotide kinase can be used to remove the 3′ phosphate group.

Another method of synthesizing oligonucleotide tags is depicted in FIG.11B. As shown in FIG. 11B, an oligonucleotide tag (1128) can besynthesized by ligating two oligonucleotide fragments (1121 and 1127).One oligonucleotide fragment (1121) may comprise a universal primerbinding site (1122), unique identifier region (1123) and a left splint(1123). The other oligonucleotide fragment (1128) may comprise a rightsplint (1125) and a target specific region (1126). A ligase (e.g., T4DNA ligase) can be used to join the two oligonucleotide fragments (1121and 1127) to produce an oligonucleotide tag (1128). Double strandedligation of the left splint (1124) and right splint (1125) can producean oligonucleotide tag (1128) with a bridge splint (1129).

An alternative method of synthesizing an oligonucleotide tag by ligatingtwo oligonucleotide fragments is depicted in FIG. 11C. As shown in FIG.11C, an oligonucleotide tag (1158) is synthesized by ligating twooligonucleotide fragments (1150 and 1158). One oligonucleotide fragment(1150) may comprise a universal primer binding site (1151), uniqueidentifier region (1152), and a ligation sequence (1153). The otheroligonucleotide fragment (1158) may comprise a ligation sequence (1154)that is complementary to the ligation sequence (1153) of the firstoligonucleotide fragment (1150), a complement of a target specificregion (1155), and a label (1156). The oligonucleotide fragment (1159)may also comprise a 3′ phosphate which prevents extension of theoligonucleotide fragment. As shown in Step 1 of FIG. 11C, the ligationsequences (1153 and 1154) of the two oligonucleotide fragments mayanneal and a polymerase can be used to extend the 3′ end of the firstoligonucleotide fragment (1150) to produce an oligonucleotide tag(1158). The oligonucleotide tag (1158) may comprise a universal primerbinding site (1151), unique identifier region (1152), ligation sequence(1153), and a target specific sequence (1157). The target specificsequence (1157) of the oligonucleotide tag (1158) may be the complementof the complement of the target specific region (1155) of the secondoligonucleotide fragment (1159). The oligonucleotide fragment comprisingthe label (1156) can be removed from the oligonucleotide tags (1158).For example, the label (1156) may comprise biotin and oligonucleotidefragments (1159) comprising the biotin label (1156) can be removed viastreptavidin capture. In another example, the label (1156) may comprisea 5′ phosphate and oligonucleotide fragments (1159) comprising the 5′phosphate (1156) can be removed via an exonuclease (e.g., Lambdaexonuclease).

As depicted in FIG. 11D, a first oligonucleotide fragment (1170)comprising a universal primer binding site (1171), unique identifierregion (1172), a first ligation sequence (1173) is annealed to a secondoligonucleotide fragment (1176) comprising a second ligation sequence(1174) and an RNA complement of the target sequence (1175). Step 1 maycomprise annealing the first and second ligation sequences (1173 and1174) followed by reverse transcription of the RNA complement of thetarget sequence (1175) to produce an oligonucleotide tag (1177)comprising a universal primer binding site (1171), unique identifierregion (1172), a first ligation sequence (1173), and a target specificregion (1178). The oligonucleotide fragments comprising the RNAcomplement of the target sequence can be selectively degraded by RNAsetreatment.

The oligonucleotide tag can comprise at least about 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70,80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotidesor base pairs. In another example, the oligonucleotide tag comprises atleast about 1500, 2,000; 2500, 3,000; 3500, 4,000; 4500, 5,000; 5500,6,000; 6500, 7,000; 7500, 8,000; 8500, 9,000; 9500, or 10,000nucleotides or base pairs.

The tags can be hexamers, e.g. random hexamers. The tags can be randomlygenerated from a set of mononucleotides. The tags can be assembled byrandomly incorporating mononucleotides.

The tags can also be assembled without randomness, to generate a libraryof different tags which are not randomly generated but which includessufficient numbers of different tags to practice the methods.

In some embodiments an oligonucleotide tag can comprise a cutback in atarget molecule. The cutback can be, for example, a enzymatic digestionof one or both ends of a target molecule. The cutback can be used inconjunction with the addition of added oligonucleotide tags. Thecombination of the cutback and the added tags can contain informationrelated to the particular starting molecule. By adding a random cutbackto the tag a smaller diversity of the added tags may be necessary forcounting the number of target molecules when detection allows adetermination of both the random cutback and the added oligonucleotides.

The oligonucleotide tag can comprise a target specific region. Thetarget specific region can comprise a sequence that is complementary tothe molecule. In some instances, the molecule is an mRNA molecule andthe target specific region comprises an oligodT sequence that iscomplementary to the polyA tail of the mRNA molecule. The targetspecific region can also act as a primer for DNA and/or RNA synthesis.For example, the oligodT sequence of the target specific region can actas a primer for first strand synthesis of a cDNA copy of the mRNAmolecule. Alternatively, the target specific region comprises a sequencethat is complementary to any portion of the molecule. In otherinstances, the target specific region comprises a random sequence thatcan be hybridized or ligated to the molecule. The target specific regioncan enable attachment of the oligonucleotide tag to the molecule.Attachment of the oligonucleotide tag can occur by any of the methodsdisclosed herein (e.g., hybridization, ligation). In some instances, thetarget specific region comprises a sequence that is recognized by one ormore restriction enzymes. The target specific region can comprise atleast about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600,700, 800, 900, or 1000 nucleotides or base pairs. In another example,the target specific region comprises at least about 1500, 2000, 2500,3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500,9000, 9500, or 10000 nucleotides or base pairs. Preferably, the targetspecific region comprises at least about 5-10, 10-15, 10-20, 10-30,15-30, or 20-30 nucleotides or base pairs.

In some instances, the target specific region is specific for aparticular gene or gene product. For example, the target specific regioncomprises a sequence complementary to a region of a p53 gene or geneproduct. Therefore, the oligonucleotide tags can only attach tomolecules comprising the p53-specific sequence. Alternatively, thetarget specific region is specific for a plurality of different genes orgene products. For example, the target specific region comprises anoligodT sequence. Therefore, the oligonucleotide tags can attach to anymolecule comprising a polyA sequence. In another example, the targetspecific region comprises a random sequence that is complementary to aplurality of different genes or gene products. Thus, the oligonucleotidetag can attach to any molecule with a sequence that is complementary tothe target specific region. In other instances, the target specificregion comprises a restriction site overhang (e.g., EcoRI sticky-endoverhang). The oligonucleotide tag can ligate to any molecule comprisinga sequence complementary to the restriction site overhang.

The oligonucleotide tag disclosed herein often comprises a uniqueidentifier region. The unique identifier region may be used to uniquelyidentify occurrences of target species thereby marking each species withan identifier that can be used to distinguish between two otherwiseidentical or nearly identical targets. The unique identifier region ofthe plurality of oligonucleotide tags can comprise a collection ofdifferent semiconductor nanocrystals, metal compounds, peptides,oligonucleotides, antibodies, small molecules, isotopes, particles orstructures having different shapes, colors, barcodes or diffractionpatterns associated therewith or embedded therein, strings of numbers,random fragments of proteins or nucleic acids, different isotopes, orany combination thereof. The unique identifier region can comprise adegenerative sequence. The unique identifier region can comprise atleast about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600,700, 800, 900, or 1000 nucleotides or base pairs. In another example,the unique identifier region comprises at least about 1500; 2,000; 2500,3,000; 3500, 4,000; 4500, 5,000; 5500, 6,000; 6500, 7,000; 7500, 8,000;8500, 9,000; 9500, or 10,000 nucleotides or base pairs. Preferably, theunique identifier region comprises at least about 10-30, 15-40, or 20-50nucleotides or base pairs.

In some instances, the oligonucleotide tag comprises a universal primerbinding site. The universal primer binding site allows the attachment ofa universal primer to the labeled-molecule and/or labeled-amplicon.Universal primers are well known in the art and include, but are notlimited to, −47F (M13F), alfaMF, AOX3′, AOX5′, BGH_r, CMV_(—)−30,CMV_(—)−50, CVM_f, LACrmt, lamgda gt 10F, lambda gt 10R, lambda gt 11F,lambda gt 11R, M13 rev, M13Forward(−20), M13Reverse, male, p10SEQP_pQE,pA_(—)−120, pet_(—)4, pGAP Forward, pGL_RVpr3, pGLpr2_R, pKLAC1_(—)4,pQE_FS, pQE_RS, puc_U1, puc_U2, revers_A, seq_IRES_tam, seq_IRES_zpet,seq_ori, seq_PCR, seq_pIRES−, seq_pIRES+, seq_pSecTag, seq_pSecTag+,seq_retro+PSI, SP6, T3-prom, T7-prom, and T7-term_Inv. Attachment of theuniversal primer to the universal primer binding site can be used foramplification, detection, and/or sequencing of the labeled-moleculeand/or labeled-amplicon. The universal primer binding site can compriseat least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500,600, 700, 800, 900, or 1000 nucleotides or base pairs. In anotherexample, the universal primer binding site comprises at least about1500; 2,000; 2500, 3,000; 3500, 4,000; 4500, 5,000; 5500, 6,000; 6500,7,000; 7500, 8,000; 8500, 9,000; 9500, or 10,000 nucleotides or basepairs. Preferably, the universal primer binding site comprises 10-30nucleotides or base pairs.

The oligonucleotide tag may comprise an adapter region. The adapterregion may enable hybridization of one or more probes. The adapterregion may enable hybridization of one or more HCR probes.

The oligonucleotide tag may comprise one or more labels.

The oligonucleotide tag may act as an initiator for a hybridizationchain reaction (HCR). The adapter region of the oligonucleotide tag mayact as an initiation for HCR. The universal primer binding site may actas an initiator for HCR.

In some instances, the oligonucleotide tag is single-stranded. In otherinstances, the oligonucleotide tag is double-stranded. Theoligonucleotide tag can be linear. Alternatively, the oligonucleotidetag comprises a secondary structure. As used herein, “secondarystructure” includes tertiary, quaternary, etc. . . . structures. In someinstances, the secondary structure is a hairpin, a stem-loop structure,an internal loop, a bulge loop, a branched structure or a pseudoknot,multiple stem loop structures, cloverleaf type structures or any threedimensional structure. In some instances, the secondary structure is ahairpin. The hairpin can comprise an overhang sequence. The overhangsequence of the hairpin can act as a primer for a polymerase chainreaction and/or reverse transcription reaction. The overhang sequencecomprises a sequence that is complementary to the molecule to which theoligonucleotide tag is attached and the overhang sequence hybridizes tothe molecule. The overhang sequence can be ligated to the molecule andacts as a template for a polymerase chain reaction and/or reversetranscription reaction. In some embodiments the tag comprises nucleicacids and/or synthetic nucleic acids and/or modified nucleic acids.

An oligonucleotide tag comprising a hairpin may act as a probe for ahybridization chain reaction. Further disclosed herein is a stochasticlabel-based hybridization chain reaction (HCR) method comprisingstochastically labeling one or more nucleic acid molecules with anoligonucleotide tag, wherein the oligonucleotide tag is a hairpin andthe one or more nucleic acid molecules act as initiators for ahybridization chain reaction. A schematic of a stochastic label-basedhybridization reaction is depicted in FIG. 34. As shown in FIG. 34, oneor more nucleic acid molecules (3480) are stochastically labeled with aplurality of hairpin oligonucleotide tags (3490) by initiating ahybridization chain reaction. The hairpin oligonucleotide tags maycomprise one or more labels (3410, 3470), an overhang (3420, 3420′), astem (3430, 3460), and a loop (3450). The overhang region (3420) of thehairpin oligonucleotide tag (3490) may comprise a target specificregion. The overhang region (3420) may comprise an oligodT sequence. Thesample comprising the one or more nucleic acid molecules may be treatedwith one or more restriction nucleases prior to stochastic labeling. Theoverhang region (3420) may comprise a restriction enzyme recognitionsequence. The sample comprising the one or more nucleic acid moleculesmay be contacted with one or more adapters prior to stochastic labelingto produce an adapter-nucleic acid molecule hybrid. The overhang region(3420) and the stem (3430) may be complementary to the one or moreadapters. The loop (3450) of the oligonucleotide tag may comprise aunique identifier region. Hybridization of a first hairpinoligonucleotide tag (3490) to the nucleic acid molecules (3480) mayresult in the formation of a labeled molecule (3415), wherein the firsthairpin oligonucleotide tag is linearized to produce a first linearizedoligonucleotide tag. The first linearized oligonucleotide tag of labeledmolecule (3415) can act as an initiator for hybridization of a secondhairpin oligonucleotide tag to the labeled molecule (3415) to produce alabeled molecule with two linearized oligonucleotide tags (3425). Thesecond linearized oligonucleotide tag can act as an initiator foranother hybridization reaction. This process can be repeated multipletimes to produce a labeled molecule with multiple linearized HCR probes(3435). The labels (3410, 3470) on the HCR probe can enable detection ofthe labeled molecule. The labels (3410, 3470) may be any type of label(e.g., fluorophore, chromophore, small molecule, nanoparticle, hapten,enzyme, antibody, magnet). The labels (3360 and 3390) may comprisefragments of a single label. The labels (3410, 3470) may generate adetectable signal when they are in close proximity. When theoligonucleotide tag is a hairpin, the labels (3360 and 3390) may be toofar away to produce a detectable signal. When the hairpinoligonucleotide tag is linearized and multiple linearized hairpinoligonucleotide tags are hybridized together, the labels (3410, 3470)may be in close enough proximity to generate a detectable signal. Forexample, a hairpin oligonucleotide tag (3350) may comprise two pyrenemoieties as labels (3410, 3470). Alternatively, the labels may benanoparticles. The stochastic label-based HCR can enable attachment ofmultiple hairpin oligonucleotide tags to a labeled molecule, which canresult in signal amplification. Stochastic label-based HCR may increasethe sensitivity of detection, analysis and/or quantification of thenucleic acid molecules. Stochastic label-based HCR may increase theaccuracy of detection, analysis, and/or quantification of one or morenucleic acid molecules.

In some instances, the plurality of oligonucleotide tags comprises atleast about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 different oligonucleotidetags. In other instances, the plurality of oligonucleotide tagscomprises at least about 200; 300; 400; 500; 600; 700; 800; 900; 1,000;2,000; 3,000; 4,000; 5,000; 6,000; 7,000; 8,000; 9,000; or 10000different oligonucleotide tags. Alternatively; the plurality ofoligonucleotide tags comprises at least about 20,000; 30,000; 40,000;50,000; 60,000; 70,000; 80,000; 90,000; or 100,000 differentoligonucleotide tags.

The number of oligonucleotide tags in the plurality of oligonucleotidetags is often in excess of the number of molecules to be labeled. Insome instances, the number of oligonucleotide tags in the plurality ofoligonucleotide tags is at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 30, 40, 50, 60, 70, 80, 90, or 100 times greater than the number ofmolecules to be labeled.

The number of different oligonucleotide tags in the plurality ofoligonucleotide tags is often in excess of the number of differentmolecules to be labeled. In some instances, the number of differentoligonucleotide tags in the plurality of oligonucleotide tags is atleast about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 15, 20,30, 40, 50, 60, 70, 80, 90, or 100 times greater than the number ofdifferent molecules to be labeled.

In some instances, stochastic labeling of a molecule comprises aplurality of oligonucleotide tags, wherein the concentration of thedifferent oligonucleotide tags in the plurality of oligonucleotide tagsis the same. In such instances, the plurality of oligonucleotide tagscomprises equal numbers of each different oligonucleotide tag.Additionally, the relative ratio of the different oligonucleotide tagsin the plurality of oligonucleotide is 1:1:1 . . . 1.

In some instances, stochastic labeling of a molecule comprises aplurality of oligonucleotide tags, wherein the concentration of thedifferent oligonucleotide tags in the plurality of oligonucleotide tagsis different. In such instances, the plurality of oligonucleotide tagscomprises different numbers of each different oligonucleotide tag.Additionally, the relative ratio of the different oligonucleotide tagsin the plurality of oligonucleotide is not 1:1:1 . . . 1. In someinstances, some oligonucleotide tags are present at higherconcentrations than other oligonucleotide tags in the plurality ofoligonucleotide tags. In some instances, stochastic labeling withdifferent concentrations of oligonucleotide tags extends the samplemeasurement dynamic range without increasing the number of differentlabels used. For example, consider stochastically labeling 3 nucleicacid sample molecules with 10 different oligonucleotide tags all atequal concentration. We expect to observe 3 different labels. Nowinstead of 3 nucleic acid molecules, consider 30 nucleic acid molecules,and we expect to observe all 10 labels. In contrast, if we still used 10different stochastic labels and alter the relative ratios of the labelsto 1:2:3:4 . . . 10, then with 3 nucleic acid molecules, we would expectto observe between 1-3 labels, but with 30 molecules we would expect toobserve only approximately 5 labels thus extending the range ofmeasurement with the same number of stochastic labels.

The relative ratios of the different oligonucleotide tags in theplurality of oligonucleotide tags can be 1:X, where X is at least about1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60,65, 70, 75, 80, 85, 90, 95, or 100. Alternatively, the relative ratiosof “n” different oligonucleotide tags in the plurality ofoligonucleotide tags is 1:A:B:C: . . . Z_(n), where A, B, C . . . Z_(n)is at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100.

In some instances, the concentration of two or more differentoligonucleotide tags in the plurality of oligonucleotide tags is thesame. For “n” different oligonucleotide tags, the concentration of atleast 2, 3, 4, . . . n different oligonucleotide tags is the same.Alternatively, the concentration of two or more differentoligonucleotide tags in the plurality of oligonucleotide tags isdifferent. For “n” different oligonucleotide tags, the concentration ofat least 2, 3, 4, . . . n different oligonucleotide tags is different.In some instances, for “n” different oligonucleotide tags, thedifference in concentration for at least 2, 3, 4, . . . n differentoligonucleotide tags is at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7, 0.8, 0.9, 1, 1.25, 1.5, 1.75, 2, 2.25, 2.5, 2.75, 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600,700, 800, 900, or 1000-fold.

In some instances, at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 95%, 97%, or 100% of the different oligonucleotide tagsin the plurality of oligonucleotide tags have the same concentration.Alternatively, at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, or 100% of the different oligonucleotide tags in theplurality of oligonucleotide tags have a different concentration.

The sequences of the oligonucleotide tags may be optimized to minimizedimerization of oligonucleotide tags. FIG. 15 depicts the formation ofoligonucleotide tag dimers when the oligonucleotide tag sequences arenot optimized. As shown in FIG. 15, when oligonucleotide tag sequencesare not optimized, a first oligonucleotide tag (1507) comprising auniversal primer binding site (1501), a first unique identifier region(1502) and a first target specific region (1503) can anneal to a secondoligonucleotide tag (1508) comprising a universal primer binding site(1501), a second unique identifier region (1504) and a second targetspecific region (1505). The oligonucleotide tag dimer can be amplifiedand result in the formation of an amplicon (1506) comprising twouniversal primer binding sites on each end of the amplicon and a targetspecific region and a unique identifier region. Because theconcentration of the oligonucleotide tags are far greater that thenumber of DNA templates, these oligonucleotide tag dimers can outcompetethe labeled DNA molecules in an amplification reaction. Unamplified DNAslead to false negatives, and amplified oligonucleotide tag dimers leadto high false positives. Thus, the oligonucleotide tags can be optimizedto minimize oligonucleotide tag dimer formation. Alternatively,oligonucleotide tags that dimerize are discarded, thereby eliminatingoligonucleotide tag dimer formation.

Alternatively, as depicted in FIG. 16, oligonucleotide tag dimerformation can be eliminated or reduced by incorporating one or moremodifications into the oligonucleotide tag sequence. As shown in FIG.16, an oligonucleotide tag (1610) comprising a universal primer bindingsite (1611), unique identifier region (1612), and target specific region(1613) comprising uracils and a 3′ phosphate group is annealed to atarget molecule (1616). The target molecule (1616) may be a restrictionendonuclease digested fragment. The restriction endonuclease mayrecognize the recognition site depicted in FIG. 16. PCR amplificationmay comprise one or more forward primers (1618 and 1618) and one or morereverse primers (1614 and 1615). PCR amplification may comprise nestedPCR with a forward primer (1618) specific for the universal primerbinding site (1611) of the oligonucleotide tag and a forward primer(1617) specific for the target specific region (1613) of theoligonucleotide tag and reverse primers (1614 and 1615) that arespecific for the target molecule. The target molecule can be amplifiedusing a Pfu DNA polymerase, which cannot amplify template comprising oneor more uracils. Thus, any dimerized oligonucleotide tags cannot beamplified by Pfu DNA polymerase.

VIII. Detectable Labels

The methods, kits, and systems disclosed herein can further comprise adetectable label. The terms “detectable label” or “label” can be usedinterchangeabley and refer to any chemical moiety attached to anucleotide, nucleotide polymer, or nucleic acid binding factor, whereinthe attachment may be covalent or non-covalent. Preferably, the label isdetectable and renders the nucleotide or nucleotide polymer detectableto the practitioner of the invention. Detectable labels that may be usedin combination with the methods disclosed herein include, for example, afluorescent label, a chemiluminescent label, a quencher, a radioactivelabel, biotin, pyrene moiety, gold, or combinations thereof.Non-limiting example of detectable labels include luminescent molecules,fluorochromes, fluorescent quenching agents, colored molecules,radioisotopes or scintillants.

In some instances, the methods disclosed herein further compriseattaching one or more detectable labels to the labeled-molecule or anyproduct thereof (e.g., labeled-amplicon). The methods can compriseattaching two or more detectable labels to the labeled-molecule.Alternatively, the method comprises attaching at least about 3, 4, 5, 6,7, 8, 9, or 10 detectable labels to a labeled-molecule. In someinstances, the detectable label is a Cy™ label. The Cy™ label is a Cy3label. Alternatively, or additionally, the detectable label is biotin.In some embodiments the detectable label is attached to a probe whichbinds the molecule or labeled molecule. This can occur, for example,after the molecule or labeled molecule has been hybridized to an array.In one example the molecule is bound to partners on an array. After thebinding a probe with can bind the molecule is bound to the molecules onthe array. This process can be repeated with multiple probes and labelsto decrease the likelihood that a signal is the result of nonspecificbinding of a label or nonspecific binding of the molecule to the array.

In some instances a donor acceptor pair can be used as the detectablelabels. Either the donor or acceptor can be attached to a probe thatbinds a nucleic acid. The probe can be, for example, a nucleic acidprobe that can bind to a the molecule or the labeled molecule. Thecorresponding donor or acceptor can be added to cause a signal.

In some instances, the detectable label is a Freedom dye, Alexa Fluor®dye, Cy™ dye, fluorescein dye, or LI-COR IRDyes®. In some instances, theFreedom dye is fluorescein (6-FAM™, 6-carboxyfluoroscein), MAX (NHSEster), TYE™ 563, TEX 615, TYE™ 665, TYE 705. The detectable label canbe an Alexa Fluor dye. Examples of Alexa Fluor® dyes include AlexaFluor® 488 (NHS Ester), Alexa Fluor® 532 (NHS Ester), Alexa Fluor® 546(NHS Ester), Alexa Fluor® 594 (NHS Ester), Alexa Fluor® 647 (NHS Ester),Alexa Fluor® 660 (NHS Ester), or Alexa Fluor® 750 (NHS Ester).Alternatively, the detectable label is a Cy™ dye. Examples of Cy™ dyesinclude, but are not limited to, Cy2, Cy3, Cy3B, Cy3.5, Cy5, Cy5.5, andCy7. In some instances, the detectable label is a fluorescein dye.Non-limiting examples of fluorescein dyes include 6-FAM™ (Azide), 6-FAM™(NHS Ester), Fluorescein dT, JOE (NHS Ester), TET™, and HEX™. In someinstances, the detectable label is a LI-COR IRDyes®, such as 5′ IRDye®700, 5′ IRDye® 800, or IRDye® 800CW (NHS Ester). In some instances, thedetectable label is TYE™ 563. Alternatively, the detectable label isCy3.

The detectable label can be Rhodamine dye. Examples of rhodamine dyesinclude, but are not limited to, Rhodamine Green™-X (NHS Ester), TAMRA™,TAMRA™ (NHS Ester), Rhodamine Red™-X(NHS Ester), ROX™ (NHS Ester), and5′TAMRA™ (Azide). In other instances, the detectable label is a WellREDDye. WellRED Dyes include, but are not limited to, WellRED D4 dye,WellRED D3 dye, and WellRED D2 dye. In some instances, the detectablelabel is Texas Red®-X (NHS Ester), Lightcycler® 640 (NHS Ester), or Dy750 (NHS Ester).

In some instances, detectable labels include a linker molecule. Examplesof linker molecules include, but are not limited to, biotin, avidin,streptavidin, HRP, protein A, protein G, antibodies or fragmentsthereof, Grb2, polyhistidine, Ni²+, FLAG tags, myc tags. Alternatively,detectable labels include heavy metals, electron donors/acceptors,acridinium esters, dyes and calorimetric substrates. In other instances,detectable labels include enzymes such as alkaline phosphatase,peroxidase and luciferase.

A change in mass can be considered a detectable label, as is the case ofsurface plasmon resonance detection. The skilled artisan would readilyrecognize useful detectable labels that are not mentioned herein, whichmay be employed in the operation of the present invention.

In some instances, detectable labels are used with primers. For example,the universal primer is a labeled with the detectable label (e.g., Cy3labeled universal primer, fluorophore labeled universal primer).Alternatively, the target specific primer is labeled with the detectablelabel (e.g., TYE 563-labeled target specific primer). In otherinstances, detectable labels are used with the oligonucleotide tags. Forexample, the oligonucleotide tag is labeled with a detectable label(e.g., biotin-labeled oligonucleotide tag). In other instances,detectable labels are used with the nucleic acid template molecule.Detectable labels can be used to detect the labeled-molecules orlabeled-amplicons. Alternatively, detectable labels are used to detectthe nucleic acid template molecule.

In some instances, the detectable label is attached to the primer,oligonucleotide tag, labeled-molecule, labeled-amplicon, probe, HCRprobe, and/or non-labeled molecule. Methods for attaching the detectablelabel to the primer, oligonucleotide tag, labeled-molecule,labeled-amplicon, and/or non-labeled molecule include, but are notlimited to, chemical labeling and enzymatic labeling. In some instances,the detectable label is attached by chemical labeling. In someembodiments, chemical labeling techniques comprise a chemically reactivegroup. Non-limiting examples of reactive groups include amine-reactivesuccinimidyl esters such as NHS-fluorescein or NHS-rhodamine,amine-reactive isothiocyanate derivatives including FITC, andsulfhydryl-reactive maleimide-activated fluors such asfluorescein-5-maleimide. In some embodiments, reaction of any of thesereactive dyes with another molecule results in a stable covalent bondformed between a fluorophore and the linker and/or agent. In someembodiments, the reactive group is isothiocyanates. In some embodiments,a label is attached to an agent through the primary amines of lysineside chains. In some embodiments, chemical labeling comprises aNHS-ester chemistry method.

Alternatively, the detectable label is attached by enzymatic labeling.Enzymatic labeling methods can include, but are not limited to, a biotinacceptor peptide/biotin ligase (AP/Bir A), acyl carrierprotein/phosphopantetheine transferase (ACP/PPTase), humanO⁶-alkylguanine transferase (hAGT), Q-tag/transglutaminase (TGase),aldehyde tag/formylglycine-generating enzyme, mutated prokaryoticdehalogenase (HaloTag™), and farnesylation motif/proteinfarnesyltransferase (PFTase) methods. Affinity labeling can include, butis not limited to, noncovalent methods utilizing dihydrofolate reductase(DHFR) and Phe36Val mutant of FK506-binding protein 12 (FKBP12(F36V)),and metal-chelation methods.

Crosslinking reagents can be used to attach a detectable label to theprimer, oligonucleotide tag, labeled-molecule, labeled-amplicon, and/ornon-labeled molecule. In some instances, the crosslinking reagent isglutaraldehyde. Glutaraldehyde can react with amine groups to createcrosslinks by several routes. For example, under reducing conditions,the aldehydes on both ends of glutaraldehyde couple with amines to formsecondary amine linkages.

In some instances, attachment of the detectable label to the primer,oligonucleotide tag, labeled-molecule, labeled-amplicon, and/ornon-labeled molecule comprises periodate-activation followed byreductive amination. In some instances, Sulfo-SMCC or otherheterobifunctional crosslinkers are used to conjugate the detectable tothe primer, oligonucleotide tag, labeled-molecule, labeled-amplicon,and/or non-labeled molecule. For example, Sulfo-SMCC is used toconjugate an enzyme to a drug. In some embodiments, the enzyme isactivated and purified in one step and then conjugated to the drug in asecond step. In some embodiments, the directionality of crosslinking islimited to one specific orientation (e.g., amines on the enzyme tosulfhydryl groups on the antibody).

IX. Supports

In some instances, the methods, kits, and systems disclosed hereincomprise a support. The term “support” and “substrate” as used hereinare used interchangeably and refer to a material or group of materialshaving a rigid or semi-rigid surface or surfaces. The support orsubstrate can be a solid support. Alternatively, the support is anon-solid support. The support or substrate can comprise a membrane,paper, plastic, coated surface, flat surface, glass, slide, chip, or anycombination thereof. In many embodiments, at least one surface of thesolid support will be substantially flat, although in some embodimentsit may be desirable to physically separate synthesis regions fordifferent compounds with, for example, wells, raised regions, pins,etched trenches, or the like. According to other embodiments, the solidsupport(s) will take the form of beads, resins, gels, microspheres, orother geometric configurations. Alternatively, the solid support(s)comprises silica chips, microparticles, nanoparticles, plates, andarrays. Methods and techniques applicable to polymer (including protein)array synthesis have been described in U.S. Patent Pub. No. 20050074787,WO 00/58516, U.S. Pat. Nos. 5,143,854, 5,242,974, 5,252,743, 5,324,633,5,384,261, 5,405,783, 5,424,186, 5,451,683, 5,482,867, 5,491,074,5,527,681, 5,550,215, 5,571,639, 5,578,832, 5,593,839, 5,599,695,5,624,711, 5,631,734, 5,795,716, 5,831,070, 5,837,832, 5,856,101,5,858,659, 5,936,324, 5,968,740, 5,974,164, 5,981,185, 5,981,956,6,025,601, 6,033,860, 6,040,193, 6,090,555, 6,136,269, 6,269,846 and6,428,752, in PCT Publication No. WO 99/36760 and WO 01/58593, which areall incorporated herein by reference in their entirety for all purposes.Patents that describe synthesis techniques in specific embodimentsinclude U.S. Pat. Nos. 5,412,087, 6,147,205, 6,262,216, 6,310,189,5,889,165, and 5,959,098. Nucleic acid arrays are described in many ofthe above patents, but many of the same techniques may be applied topolypeptide arrays. Additional exemplary substrates are disclosed inU.S. Pat. No. 5,744,305 and US Patent Pub. Nos. 20090149340 and20080038559.

In some instances, the solid support is a bead. Examples of beadsinclude, but are not limited to, streptavidin beads, agarose beads,magnetic beads, Dynabeads®, MACS® microbeads, antibody conjugated beads(e.g., anti-immunoglobulin microbead), protein A conjugated beads,protein G conjugated beads, protein A/G conjugated beads, protein Lconjugated beads, oligo-dT conjugated beads, silica beads, silica-likebeads, anti-biotin microbead, anti-fluorochrome microbead, and BcMag™Carboxy-Terminated Magnetic Beads.

The solid support can be an array or microarray. The solid support cancomprise discrete regions. The solid support can be an addressablearray. In some instances, the array comprises a plurality of probesfixed onto a solid surface. The plurality of probes enableshybridization of the labeled-molecule and/or labeled-amplicon to thesolid surface. The plurality of probes comprises a sequence that iscomplementary to at least a portion of the labeled-molecule and/orlabeled-amplicon. In some instances, the plurality of probes comprises asequence that is complementary to the oligonucleotide tag portion of thelabeled-molecule and/or labeled-amplicon. In other instances, theplurality of probes comprises a sequence that is complementary to thejunction formed by the attachment of the oligonucleotide tag to themolecule.

The array can comprise one or more probes. The probes can be in avariety of formats as depicted in FIG. 18. As shown in FIGS. 18A-18C,18G and 18H, the array (1801, 1806, 1811, 1828, 1832) can comprise aprobe (1804, 1809, 1814, 1836, 1835) comprising a sequence that iscomplementary to at least a portion of the target molecule (1802, 1807,1813, 1829, 1833) and a sequence that is complementary to the uniqueidentifier region of an oligonucleotide tag (1803, 1808, 1812, 1830,1834). As shown FIGS. 18A-18B, 18G and 18H, the sequence that iscomplementary to at least a portion of the target molecule (1802, 1807,1829, 1833) can be attached to the array. As shown in FIG. 18C, thesequence that is complementary to the unique identifier region (1812)can be attached to the array. As shown in FIG. 18D-18F, the array (1816,1820, 1824) can comprise a first probe (1817, 1821, 1825) comprising asequence that is complementary to at least a portion of the targetmolecule and a second probe (1819, 1823, 1827) that is complementary tothe unique identifier region. FIG. 18A-18H also depict the various waysin which a stochastically labeled molecule (1805, 1810, 1815, 1818,1822, 1826, 1831, 1837) can hybridize to the arrays. For example, asshown in FIGS. 18A and 18C, the junction of the unique identifier regionand the target molecule of the stochastically labeled molecule (1805,1815) can hybridize to the probe (1804, 1814) on the array. As shown inFIG. 18B, 18D-18H, there can be a gap in the regions of thestochastically labeled molecule (1810, 1818, 1822, 1826, 1831, 1837)that can hybridize to the probe on the array. As shown in FIGS. 18D-18Fand 18H, different regions of the stochastically labeled molecule (1818,1822, 1826, 1837) can hybridize to two or more probes on the array.Thus, the array probes can be in many different formats. The arrayprobes can comprise a sequence that is complementary to a uniqueidentifier region, a sequence that is complementary to the targetmolecule, or a combination thereof. Hybridization of the stochasticallylabeled molecule to the array can occur by a variety of ways. Forexample, two or more nucleotides of the stochastically labeled moleculecan hybridize to one or more probes on the array. The two or morenucleotides of the stochastically labeled molecule that hybridize to theprobes may be consecutive nucleotides, non-consecutive nucleotides, or acombination thereof. The stochastically labeled molecule that ishybridized to the probe can be detected by any method known in the art.For example, the stochastically labeled molecules can be directlydetected. Directly detecting the stochastically labeled molecule maycomprise detection of a fluorophore, hapten, or detectable label. Thestochastically labeled molecules can be indirectly detected. Indirectdetection of the stochastically labeled molecule may comprise ligationor other enzymatic or non-enzymatic methods.

The array can be in a variety of formats. For example, the array can bein a 16-, 32-, 48-, 64-, 80-, 96-, 112-, 128-, 144-, 160-, 176-, 192-,208-, 224-, 240-, 256-, 272-, 288-, 304-, 320-, 336-, 352-, 368-, 384-,or 400-format. Alternatively, the array is in an 8×60K, 4×180K, 2×400K,1×1M format. In other instances, the array is in an 8×15K, 4×44K,2×105K, 1×244K format.

The array can comprise a single array. The single array can be on asingle substrate. Alternatively, the array is on multiple substrates.The array can comprise multiple formats. The array can comprise aplurality of arrays. The plurality of arrays can comprise two or morearrays. For example, the plurality of arrays can comprise at least about2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 arrays.In some instances, at least two arrays of the plurality of arrays areidentical. Alternatively, at least two arrays of the plurality of arraysare different.

In some instances, the array comprises symmetrical chambered areas. Forexample, the array comprises 0.5×0.5 mm, 1×1 mm, 1.5×1.5 mm, 2×2 mm,2.5×2.5 mm, 3×3 mm, 3.5×3.5 mm, 4×4 mm, 4.5×4.5 mm, 5×5 mm, 5.5×5.5 mm,6×6 mm, 6.5×6.5 mm, 7×7 mm, 7.5×7.5 mm, 8×8 mm, 8.5×8.5 mm, 9×9 mm,9.5×9.5 mm, 10×10 mm, 10.5×10.5 mm, 11×11 mm, 11.5×11.5 mm, 12×12 mm,12.5×12.5 mm, 13×13 mm, 13.5×13.5 mm, 14×14 mm, 14.5×14.5 mm, 15×15 mm,15.5×15.5 mm, 16×16 mm, 16.5×16.5 mm, 17×17 mm, 17.5×17.5 mm, 18×18 mm,18.5×18.5 mm, 19×19 mm, 19.5×19.5 mm, or 20×20 mm chambered areas. Insome instances, the array comprises 6.5×6.5 mm chambered areas.Alternatively, the array comprises asymmetrical chambered areas. Forexample, the array comprises 6.5×0.5 mm, 6.5×1 mm, 6.5×1.5 mm, 6.5×2 mm,6.5×2.5 mm, 6.5×3 mm, 6.5×3.5 mm, 6.5×4 mm, 6.5×4.5 mm, 6.5×5 mm,6.5×5.5 mm, 6.5×6 mm, 6.5×6.5 mm, 6.5×7 mm, 6.5×7.5 mm, 6.5×8 mm,6.5×8.5 mm, 6.5×9 mm, 6.5×9.5 mm, 6.5×10 mm, 6.5×10.5 mm, 6.5×11 mm,6.5×11.5 mm, 6.5×12 mm, 6.5×12.5 mm, 6.5×13 mm, 6.5×13.5 mm, 6.5×14 mm,6.5×14.5 mm, 6.5×15 mm, 6.5×15.5 mm, 6.5×16 mm, 6.5×16.5 mm, 6.5×17 mm,6.5×17.5 mm, 6.5×18 mm, 6.5×18.5 mm, 6.5×19 mm, 6.5×19.5 mm, or 6.5×20mm chambered areas.

The array can comprise at least about 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6μm, 7 μm, 8 μm, 9 μm, 10 μm, 15 μm, 20 μm, 25 μm, 30 μm, 35 μm, 40 μm,45 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80 μm, 85 μm, 90 μm, 95μm, 100 μm, 125 μm, 150 μm, 175 μm, 200 μm, 225 μm, 250 μm, 275 μm, 300μm, 325 μm, 350 μm, 375 μm, 400 μm, 425 μm, 450 μm, 475 μm, or 500 μmspots. In some instances, the array comprises 70 μm spots.

The array can comprise at least about 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6μm, 7 μm, 8 μm, 9 μm, 10 μm, 15 μm, 20 μm, 25 μm, 30 μm, 35 μm, 40 μm,45 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80 μm, 85 μm, 90 μm, 95μm, 100 μm, 125 μm, 150 μm, 175 μm, 200 μm, 225 μm, 250 μm, 275 μm, 300μm, 325 μm, 350 μm, 375 μm, 400 μm, 425 μm, 450 μm, 475 μm, 500 μm, 525μm, 550 μm, 575 μm, 600 μm, 625 μm, 650 μm, 675 μm, 700 μm, 725 μm, 750μm, 775 μm, 800 μm, 825 μm, 850 μm, 875 μm, 900 μm, 925 μm, 950 μm, 975μm, 1000 μm feature pitch. In some instances, the array comprises 161 μmfeature pitch.

The array can comprise one or more probes. In some instances, the arraycomprises at least about 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90,or 100 probes. Alternatively, the array comprises at least about 200,300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500,1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700,2800, 2900, or 3000 probes. The array can comprise at least about 3500,4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500,or 10000 probes. In some instances, the array comprises at least about960 probes. Alternatively, the array comprises at least about 2780probes. The probes can be specific for the plurality of oligonucleotidetags. The probes can be specific for at least a portion of the pluralityof oligonucleotide tags. The probes can be specific for at least about5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97% or 100% of thetotal number of the plurality of oligonucleotide tags. Alternatively,the probes are specific for at least about 5%, 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 90%, 95%, 97% or 100% of the total number of differentoligonucleotide tags of the plurality of oligonucleotide tags. In otherinstances, the probes are non-specific probes. For example, the probescan be specific for a detectable label that is attached to thelabeled-molecule. The probe can be streptavidin.

The array can be a printed array. In some instances, the printed arraycomprises one or more oligonucleotides attached to a substrate. Forexample, the printed array comprises 5′ amine modified oligonucleotidesattached to an epoxy silane substrate.

Alternatively, the array comprises a slide with one or more wells. Theslide can comprise at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70,75, 80, 85, 90, 95, or 100 wells. Alternatively, the slide comprises atleast about 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 650, 700,750, 800, 850, 900, 950, or 1000 wells. In some instances, the slidecomprises 16 wells. Alternatively, the slide comprises 96 wells. Inother instances, the slide comprises at least about 80, 160, 240, 320,400, 480, 560, 640, 720, 800, 880, or 960 wells.

In some instances, the solid support is an Affymetrix 3K tag array,Arrayjet non-contact printed array, or Applied Microarrays Inc (AMI)array. Alternatively, the support comprises a contact printer, impactprinter, dot printer, or pin printer.

The solid support can comprise the use of beads that self assemble inmicrowells. For example, the solid support comprises Illumina'sBeadArray Technology. Alternatively, the solid support comprises AbbottMolecular's Bead Array technology, and Applied Micro array's FlexiPlex™system.

In other instances, the solid support is a plate. Examples of platesinclude, but are not limited to, MSD multi-array plates, MSD Multi-Spot®plates, microplate, ProteOn microplate, AlphaPlate, DELFIA plate,IsoPlate, and LumaPlate.

X. Enzymes

The methods, kits, and systems disclosed herein comprise one or moreenzymes. Examples of enzymes include, but are not limited to, ligases,reverse transcriptases, polymerases, and restriction nucleases. In someinstances, attachment of the oligonucleotide tag to the moleculescomprises the use of one or more ligases. Examples of ligases include,but are not limited to, DNA ligases such as DNA ligase I, DNA ligaseIII, DNA ligase IV, and T4 DNA ligase, and RNA ligases such as T4 RNAligase I and T4 RNA ligase II.

The methods, kits, and systems disclosed herein can further comprise theuse of one or more reverse transcriptases. In some instances, thereverse transcriptase is a HIV-1 reverse transcriptase, M-MLV reversetranscriptase, AMV reverse transcriptase, and telomerase reversetranscriptase. In some instances, the reverse transcriptase is M-MLVreverse transcriptase.

In some instances, the methods, kits, and systems disclosed hereincomprise the use of one or more polymerases. Examples of polymerasesinclude, but are not limited to, DNA polymerases and RNA polymerases. Insome instances, the DNA polymerase is a DNA polymerase I, DNA polymeraseII, DNA polymerase III holoenzyme, and DNA polymerase IV. Commerciallyavailable DNA polymerases include, but are not limited to, Bst 2.0 DNAPolymerase, Bst 2.0 WarmStart™ DNA Polymerase, Bst DNA Polymerase,Sulfolobus DNA Polymerase IV, Taq DNA Polymerase, 9° N™m DNA Polymerase,Deep VentR™ (exo-) DNA Polymerase, Deep VentR™ DNA Polymerase, HemoKlenTaq™, LongAmp® Taq DNA Polymerase, OneTaq® DNA Polymerase, Phusion®DNA Polymerase, Q5™ High-Fidelity DNA Polymerase, Therminator™ γ DNAPolymerase, Therminator™ DNA Polymerase, Therminator™ II DNA Polymerase,Therminator™ III DNA Polymerase, VentR® DNA Polymerase, VentR® (exo-)DNA Polymerase, Bsu DNA Polymerase, phi29 DNA Polymerase, T4 DNAPolymerase, T7 DNA Polymerase, and Terminal Transferase. Alternatively,the polymerase is an RNA polymerases such as RNA polymerase I, RNApolymerase II, RNA polymerase III, E. coli Poly(A) polymerase, phi6 RNApolymerase (RdRP), Poly(U) polymerase, SP6 RNA polymerase, and T7 RNApolymerase.

In some instances, the methods, kits, and systems disclosed hereincomprise one or more restriction enzymes. Restriction enzymes includetype I, type II, type III, and type IV restriction enzymes. In someinstances, Type I enzymes are complex, multisubunit, combinationrestriction-and-modification enzymes that cut DNA at random far fromtheir recognition sequences. Generally, type II enzymes cut DNA atdefined positions close to or within their recognition sequences. Theycan produce discrete restriction fragments and distinct gel bandingpatterns. Type III enzymes are also large combinationrestriction-and-modification enzymes. They often cleave outside of theirrecognition sequences and can require two such sequences in oppositeorientations within the same DNA molecule to accomplish cleavage; theyrarely give complete digests. In some instances, type IV enzymesrecognize modified, typically methylated DNA and can be exemplified bythe McrBC and Mrr systems of E. coli.

XI. Miscellaneous Components

The methods, kits, and systems disclosed herein can comprise the use ofone or more reagents. Examples of reagents include, but are not limitedto, PCR reagents, ligation reagents, reverse transcription reagents,enzyme reagents, hybridization reagents, sample preparation reagents,and reagents for nucleic acid purification and/or isolation.

The methods, kits, and systems disclosed herein can comprise the use ofone or more buffers. Examples of buffers include, but are not limitedto, wash buffers, ligation buffers, hybridization buffers, amplificationbuffers, and reverse transcription buffers. In some instances, thehybridization buffer is a commercially available buffer, such as TMACHyb solution, SSPE hybridization solution, and ECONO™ hybridizationbuffer. The buffers disclosed herein can comprise one or moredetergents.

The methods, kits, and systems disclosed herein can comprise the use ofone or more carriers. Carriers can enhance or improve the efficiency ofone or more reactions disclosed herein (e.g., ligation reaction, reversetranscription, amplification, hybridization). Carriers can decrease orprevent non-specific loss of the molecules or any products thereof(e.g., labeled-molecule, labeled-cDNA molecule, labeled-amplicon). Forexample, the carrier can decrease non-specific loss of alabeled-molecule through absorption to surfaces. The carrier candecrease the affinity of the molecule, labeled-molecule, or any productthereof to a surface or substrate (e.g., container, eppendorf tube,pipet tip). Alternatively, the carrier can increase the affinity of themolecule or any product thereof to a surface or substrate (e.g., bead,array, glass, slide, chip). Carriers can protect the molecule or anyproduct thereof from degradation. For example, carriers can protect anRNA molecule or any product thereof from ribonucleases. Alternatively,carriers can protect a DNA molecule or any product thereof from a DNase.Examples of carriers include, but are not limited to, nucleic acidmolecules such as DNA and/or RNA, or polypeptides. Examples of DNAcarriers include plasmids, vectors, polyadenylated DNA, and DNAoligonucleotides. Examples of RNA carriers include polyadenylated RNA,phage RNA, phage MS2 RNA, E. coli RNA, yeast RNA, yeast tRNA, mammalianRNA, mammalian tRNA, short polyadenylated synthetic ribonucleotides andRNA oligonucleotides. The RNA carrier can be a polyadenylated RNA.Alternatively, the RNA carrier can be a non-polyadenylated RNA. In someinstances, the carrier is from a bacteria, yeast, or virus. For example,the carrier can be a nucleic acid molecule or a polypeptide derived froma bacteria, yeast or virus. For example, the carrier is a protein fromBacillus subtilis. In another example, the carrier is a nucleic acidmolecule from Escherichia coli. Alternatively, the carrier is a nucleicacid molecule or peptide from a mammal (e.g., human, mouse, goat, rat,cow, sheep, pig, dog, or rabbit), avian, amphibian, or reptile.

The methods, kits, and systems disclosed herein can comprise the use ofone or more control agents. Control agents can include control oligos,inactive enzymes, non-specific competitors. Alternatively, the controlagents comprise bright hybridization, bright probe controls, nucleicacid templates, spike-in templates, PCR amplification controls. The PCRamplification controls can be positive controls. In other instances, thePCR amplification controls are negative controls. The nucleic acidtemplate controls can be of known concentrations. The control agents cancomprise one or more labels.

Spike-in templates can be templates that are added to a reaction orsample. For example, a spike-in template can be added to anamplification reaction. The spike-in template can be added to theamplification reaction any time after the first amplification cycle. Insome instances, the spike-in template is added to the amplificationreaction after the 2^(nd), 3^(rd), 4^(th), 5^(th), 6^(th), 7^(th),8^(th), 9^(th), 10^(th), 11^(th), 12^(th), 13^(th), 14^(th), 15^(th),20^(th), 25^(th), 30^(th), 35^(th), 40^(th), 45^(th), or 50^(th)amplification cycle. The spike-in template can be added to theamplification reaction any time before the last amplification cycle. Thespike-in template can comprise one or more nucleotides or nucleic acidbase pairs. The spike-in template can comprise DNA, RNA, or anycombination thereof. The spike-in template can comprise one or morelabels.

The methods, kits, and systems disclosed herein can comprise the use ofone or more pipet tips and/or containers (e.g., tubes, vials, multiwellplates). In some instances, the pipet tips are low binding pipet tips.Alternatively, or additionally, the containers can be low bindingcontainers. Low binding pipet tips and low binding containers can havereduced leaching and/or subsequent sample degradation associated withsilicone-based tips and non-low binding containers. Low binding pipettips and low binding containers can have reduced sample binding ascompared to non-low binding pipet tips and containers. Examples of lowbinding tips include, but are not limited to, Corning® DeckWorks™ lowbinding tips and Avant Premium low binding graduated tips. Anon-limiting list of low-binding containers include Corning® Costar® lowbinding microcentrifuge tubes and Cosmobrand low binding PCR tubes andmicrocentrifuge tubes.

XIII. Indications

The methods disclosed herein may be used in gene expression monitoring,transcript profiling, library screening, genotyping, epigeneticanalysis, methylation pattern analysis, tumor typing, pharmacogenomics,agrigenetics, pathogen profiling and detection and diagnostics. Geneexpression monitoring and profiling methods have been shown in U.S. Pat.Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860, 6,040,138, 6,177,248and 6,309,822. Genotyping and uses therefore are shown in U.S. PatentPublication Nos. 20030036069 and 20070065816 and U.S. Pat. Nos.5,856,092, 6,300,063, 5,858,659, 6,284,460, 6,361,947, 6,368,799 and6,333,179. Other uses are embodied in U.S. Pat. Nos. 5,871,928,5,902,723, 6,045,996, 5,541,061, and 6,197,506.

Disclosed herein are methods, kits and compositions for detection,monitoring, and/or prognosis of a disease or condition in a subject.Generally, the method comprises (a) stochastically labeling a moleculeto produce a stochastically-labeled molecule; and (b) detecting and/orquantifying the stochastically-labeled molecule, thereby detecting,monitoring, and/or prognosing a disease or condition in a subject.Detecting a disease or condition can comprise diagnosing a disease orcondition.

Monitoring a disease or condition in a subject can further comprisemonitoring a therapeutic regimen. Monitoring a therapeutic regimen cancomprise determining the efficacy of a therapeutic regimen. In someinstances, monitoring a therapeutic regimen comprises administrating,terminating, adding, or altering a therapeutic regimen. Altering atherapeutic regimen can comprise increasing or reducing the dosage,dosing frequency, or mode of administration of a therapeutic regimen. Atherapeutic regimen can comprise one or more therapeutic drugs. Thetherapeutic drugs can be an anticancer drug, antiviral drug,antibacterial drug, antipathogenic drug, or any combination thereof.

A. Cancer

In some instances, the disease or condition is a cancer. The moleculesto be stochastically labeled can be from a cancerous cell or tissue. Insome instances, the cancer is a sarcoma, carcinoma, lymphoma orleukemia. Sarcomas are cancers of the bone, cartilage, fat, muscle,blood vessels, or other connective or supportive tissue. Sarcomasinclude, but are not limited to, bone cancer, fibrosarcoma,chondrosarcoma, Ewing's sarcoma, malignant hemangioendothelioma,malignant schwannoma, bilateral vestibular schwannoma, osteosarcoma,soft tissue sarcomas (e.g. alveolar soft part sarcoma, angiosarcoma,cystosarcoma phylloides, dermatofibrosarcoma, desmoid tumor, epithelioidsarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma,hemangiosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma,lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma,neurofibrosarcoma, rhabdomyosarcoma, and synovial sarcoma).

Carcinomas are cancers that begin in the epithelial cells, which arecells that cover the surface of the body, produce hormones, and make upglands. By way of non-limiting example, carcinomas include breastcancer, pancreatic cancer, lung cancer, colon cancer, colorectal cancer,rectal cancer, kidney cancer, bladder cancer, stomach cancer, prostatecancer, liver cancer, ovarian cancer, brain cancer, vaginal cancer,vulvar cancer, uterine cancer, oral cancer, penile cancer, testicularcancer, esophageal cancer, skin cancer, cancer of the fallopian tubes,head and neck cancer, gastrointestinal stromal cancer, adenocarcinoma,cutaneous or intraocular melanoma, cancer of the anal region, cancer ofthe small intestine, cancer of the endocrine system, cancer of thethyroid gland, cancer of the parathyroid gland, cancer of the adrenalgland, cancer of the urethra, cancer of the renal pelvis, cancer of theureter, cancer of the endometrium, cancer of the cervix, cancer of thepituitary gland, neoplasms of the central nervous system (CNS), primaryCNS lymphoma, brain stem glioma, and spinal axis tumors. In someinstances, the cancer is a skin cancer, such as a basal cell carcinoma,squamous, melanoma, nonmelanoma, or actinic (solar) keratosis.

In some instances, the cancer is a lung cancer. Lung cancer can start inthe airways that branch off the trachea to supply the lungs (bronchi) orthe small air sacs of the lung (the alveoli). Lung cancers includenon-small cell lung carcinoma (NSCLC), small cell lung carcinoma, andmesotheliomia. Examples of NSCLC include squamous cell carcinoma,adenocarcinoma, and large cell carcinoma. The mesothelioma may be acancerous tumor of the lining of the lung and chest cavity (pleura) orlining of the abdomen (peritoneum). The mesothelioma may be due toasbestos exposure. The cancer may be a brain cancer, such as aglioblastoma.

Alternatively, the cancer may be a central nervous system (CNS) tumor.CNS tumors may be classified as gliomas or nongliomas. The glioma may bemalignant glioma, high grade glioma, diffuse intrinsic pontine glioma.Examples of gliomas include astrocytomas, oligodendrogliomas (ormixtures of oligodendroglioma and astocytoma elements), and ependymomas.Astrocytomas include, but are not limited to, low-grade astrocytomas,anaplastic astrocytomas, glioblastoma multiforme, pilocytic astrocytoma,pleomorphic xanthoastrocytoma, and subependymal giant cell astrocytoma.Oligodendrogliomas include low-grade oligodendrogliomas (oroligoastrocytomas) and anaplastic oligodendrogliomas. Nongliomas includemeningiomas, pituitary adenomas, primary CNS lymphomas, andmedulloblastomas. In some instances, the cancer is a meningioma.

The leukemia may be an acute lymphocytic leukemia, acute myelocyticleukemia, chronic lymphocytic leukemia, or chronic myelocytic leukemia.Additional types of leukemias include hairy cell leukemia, chronicmyelomonocytic leukemia, and juvenile myelomonocytic leukemia.

Lymphomas are cancers of the lymphocytes and may develop from either Bor T lymphocytes. The two major types of lymphoma are Hodgkin'slymphoma, previously known as Hodgkin's disease, and non-Hodgkin'slymphoma. Hodgkin's lymphoma is marked by the presence of theReed-Sternberg cell. Non-Hodgkin's lymphomas are all lymphomas which arenot Hodgkin's lymphoma. Non-Hodgkin lymphomas may be indolent lymphomasand aggressive lymphomas. Non-Hodgkin's lymphomas include, but are notlimited to, diffuse large B cell lymphoma, follicular lymphoma,mucosa-associated lymphatic tissue lymphoma (MALT), small celllymphocytic lymphoma, mantle cell lymphoma, Burkitt's lymphoma,mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodalmarginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma(SMZL), extranodal marginal zone B cell lymphoma, intravascular large Bcell lymphoma, primary effusion lymphoma, and lymphomatoidgranulomatosis.

B. Pathogenic Infection

In some instances, the disease or condition is a pathogenic infection.The molecules to be stochastically labeled can be from a pathogen. Thepathogen can be a virus, bacterium, fungi, or protozoan. In someinstances, the pathogen may be a protozoan, such as Acanthamoeba (e.g.,A. astronyxis, A. castellanii, A. culbertsoni, A. hatchetti, A.polyphaga, A. rhysodes, A. healyi, A. divionensis), Brachiola (e.g., Bconnori, B. vesicularum), Cryptosporidium (e.g., C. parvum), Cyclospora(e.g., C. cayetanensis), Encephalitozoon (e.g., E. cuniculi, E. hellem,E. intestinalis), Entamoeba (e.g., E. histolytica), Enterocytozoon(e.g., E. bieneusi), Giardia (e.g., G. lamblia), Isospora (e.g, I.belli), Microsporidium (e.g., M. africanum, M ceylonensis), Naegleria(e.g., N. fowleri), Nosema (e.g., N. algerae, N. ocularum),Pleistophora, Trachipleistophora (e.g., T. anthropophthera, T hominis),and Vittaforma (e.g., V. corneae). The pathogen may be a fungus, suchas, Candida, Aspergillus, Cryptococcus, Histoplasma, Pneumocystis, andStachybotrys.

The pathogen can be a bacterium. Exemplary bacteria include, but are notlimited to, Bordetella, Borrelia, Brucella, Campylobacter, Chlamydia,Chlamydophila, Clostridium, Corynebacterium, Enterococcus, Escherichia,Francisella, Haemophilus, Helicobacter, Legionella, Leptospira,Listeria, Mycobacterium, Mycoplasma, Neisseria, Pseudomonas, Rickettsia,Salmonella, Shigella, Staphylococcus, Streptococcus, Treponema, Vibrio,or Yersinia.

The virus can be a reverse transcribing virus. Examples of reversetranscribing viruses include, but are not limited to, single strandedRNA-RT (ssRNA-RT) virus and double-stranded DNA-RT (dsDNA-RT) virus.Non-limiting examples of ssRNA-RT viruses include retroviruses,alpharetrovirus, betaretrovirus, gammaretrovirus, deltaretrovirus,epsilonretrovirus, lentivirus, spuma virus, metavirirus, andpseudoviruses. Non-limiting examples of dsDNA-RT viruses includehepadenovirus and caulimovirus. Alternatively, the virus is a DNA virusor RNA virus. The DNA virus can be a double-stranded DNA (dsDNA) virus.In some instances, the dsDNA virus is an adenovirus, herpes virus, orpox virus. Examples of adenoviruses include, but are not limited to,adenovirus and infectious canine hepatitis virus. Examples of herpesviruses include, but are not limited to, herpes simplex virus,varicella-zoster virus, cytomegalovirus, and Epstein-Barr virus. Anon-limiting list of pox viruses includes smallpox virus, cow pox virus,sheep pox virus, monkey pox virus, and vaccinia virus. The DNA virus canbe a single-stranded DNA (ssDNA) virus. The ssDNA virus can be aparvovirus. Examples of parvoviruses include, but are not limited to,parvovirus B19, canine parvovirus, mouse parvovirus, porcine parvovirus,feline panleukopenia, and Mink enteritis virus.

Alternatively, the virus is a RNA virus. The RNA virus can be adouble-stranded RNA (dsRNA) virus, (+) sense single-stranded RNA virus((+)ssRNA) virus, or (−) sense single-stranded ((−)ssRNA) virus. Anon-limiting list of dsRNA viruses include reovirus, orthoreovirus,cypovirus, rotavirus, bluetongue virus, and phytoreovirus. Examples of(+) ssRNA viruses include, but are not limited to, picornavirus andtogavirus. Examples of picornaviruses include, but are not limited to,enterovirus, rhinovirus, hepatovirus, cardiovirus, aphthovirus,poliovirus, parechovirus, erbovirus, kobuvirus, teschovirus, andcoxsackie. In some instances, the togavirus is a rubella virus, Sindbisvirus, Eastern equine encephalitis virus, Western equine encephalitisvirus, Venezuelan equine encephalitis virus, Ross River virus,O'nyong'nyong virus, Chikungunya, or Semliki Forest virus. Anon-limiting list of (−) ssRNA viruses include orthomyxovirus andrhabdovirus. Examples of orthomyxoviruses include, but are not limitedto, influenzavirus a, influenzavirus B, influenzavirus C, isavirus, andthogotovirus. Examples of rhabdoviruses include, but are not limited to,cytorhabdovirus, dichorhabdovirus, ephemerovirus, lyssavirus,novirhabdovirus, and vesiculovirus.

C. Fetal Disorders

In some instances, the disease or condition is pregnancy. The methodsdisclosed herein can comprise diagnosing a fetal condition in a pregnantsubject. The methods disclosed herein can comprise identifying fetalmutations or genetic abnormalities. The molecules to be stochasticallylabeled can be from a fetal cell or tissue. Alternatively, oradditionally, the molecules to be labeled can be from the pregnantsubject.

The methods, kits, and systems disclosed herein can be used in thediagnosis, prediction or monitoring of autosomal trisomies (e.g.,Trisomy 13, 15, 16, 18, 21, or 22). In some cases the trisomy may beassociated with an increased chance of miscarriage (e.g., Trisomy 15,16, or 22). In other cases, the trisomy that is detected is a liveborntrisomy that may indicate that an infant will be born with birth defects(e.g., Trisomy 13 (Patau Syndrome), Trisomy 18 (Edwards Syndrome), andTrisomy 21 (Down Syndrome)). The abnormality may also be of a sexchromosome (e.g., XXY (Klinefelter's Syndrome), XYY (Jacobs Syndrome),or XXX (Trisomy X). The molecule(s) to be labeled can be on one or moreof the following chromosomes: 13, 18, 21, X, or Y. For example, themolecule is on chromosome 21 and/or on chromosome 18, and/or onchromosome 13.

Further fetal conditions that can be determined based on the methods,kits, and systems disclosed herein include monosomy of one or morechromosomes (X chromosome monosomy, also known as Turner's syndrome),trisomy of one or more chromosomes (13, 18, 21, and X), tetrasomy andpentasomy of one or more chromosomes (which in humans is most commonlyobserved in the sex chromosomes, e.g. XXXX, XXYY, XXXY, XYYY, XXXXY,XXXYY, XYYYY and XXYYY), monoploidy, triploidy (three of everychromosome, e.g. 69 chromosomes in humans), tetraploidy (four of everychromosome, e.g. 92 chromosomes in humans), pentaploidy and multiploidy.

Exemplary Embodiments

Disclosed herein, in some embodiments, are methods, kits, and systemsfor digital reverse transcription of an RNA molecule. In some instances,the method comprises (a) producing a labeled-RNA molecule by contactinga sample comprising a plurality of RNA molecules with a plurality ofoligonucleotide tags, wherein (i) the plurality of RNA moleculescomprises two or more RNA molecules comprising at least two differentsequences; and (ii) the plurality of oligonucleotide tags comprisesoligonucleotide tags comprising two or more different unique identifiersequences; (b) conducting a first strand synthesis reaction bycontacting the labeled-RNA molecules with a reverse transcriptase enzymeto produce a labeled-cDNA molecule; and (c) detecting the labeled-cDNAmolecule by hybridizing the labeled-cDNA molecule to a solid support.

Producing a labeled-RNA molecule can comprise attaching theoligonucleotide tag to the RNA molecule. In some instances, theoligonucleotide tag is attached to the RNA molecule by hybridization. Inother instances, the oligonucleotide tag is attached to the RNA moleculeby ligation. The attachment of the oligonucleotide tag can comprise theuse of a ligase enzyme. The oligonucleotide tag can be attached to anyportion of the RNA molecule. For example, the oligonucleotide tag can beattached to the 5′ end of the RNA molecule. Alternatively, theoligonucleotide tag is attached to the 3′ end of the RNA molecule. Inother instances, the oligonucleotide tag is attached to an internalregion of the RNA molecule. Attachment of the oligonucleotide tag to theRNA molecule can comprise the use of one or more adaptor molecules.

In some instances, the oligonucleotide tag comprises a target specificregion. The target specific region can enable attachment of theplurality of oligonucleotide tags to at least one RNA molecule. Thetarget specific region can enable attachment of the plurality ofoligonucleotide tags to two more different RNA molecules. In someinstances, the target specific region enables attachment of theplurality of oligonucleotide tags to at least about 3, 4, or 5 differentRNA molecules. Alternatively, the target specific region enablesattachment of the plurality of oligonucleotide tags to at least about 6,7, 8, 9, or 10 different RNA molecules. In other instances, the targetspecific region enables attachment of the plurality of oligonucleotidetags to at least about 11, 12, 13, 14, or 15 different RNA molecules.The target specific region can comprise an oligodT sequence.Alternatively, the target specific region comprises a random sequencethat can attach to any portion of the RNA molecule.

In some instances, the oligonucleotide tag further comprises a universalprimer region. The unique identifier region can be placed between theuniversal primer region and the target specific region. Theoligonucleotide tag can be at least one nucleotide in length. The uniqueidentifier region can be at least one nucleotides in length. The targetspecific region can be at least one nucleotide in length. The universalprimer region can be at least one nucleotide in length. Theoligonucleotide tag can comprise one or more nucleotide moieties.Alternatively, or additionally, the nucleotide tag comprises one or morenon-nucleotide moieties.

In some instances, producing the labeled-RNA molecule further comprisesa dNTP mix, annealing buffer, ligase, ligation buffer, or anycombination thereof. Conducting the first strand synthesis reaction canfurther comprise a first strand buffer, dithiothreitol (DTT), RNaseinhibitor, DNA polymerase, or any combination thereof.

The first strand synthesis reaction can further comprise a thermalcycler. The first strand synthesis reaction can further comprise athermal cycler program comprising 1 cycle of 50° C. for 60 minutes,followed by 3 cycles of 94° C. for 2 minutes, 58° C. for 2 minutes, and68° C. for 2 minutes, followed by 1 cycle of 4° C. for at least 2minutes. The methods disclosed herein can further comprise contactingthe labeled-cDNA molecule with a target specific primer. The targetspecific primer can be a uracil-containing DNA primer. The targetspecific primer can hybridize to the labeled-cDNA molecule and apolymerase chain reaction can be conducted to produce a double-strandedlabeled-cDNA molecule.

The sample can be further treated with one or more enzymes to remove ordegrade RNA molecules, labeled-RNA molecules, unbound oligonucleotidetags, and/or unbound target specific primers. For example, the samplecan be treated with an RNase enzyme to remove the RNA molecules (labeledand/or unbound RNA molecules) from the sample. Alternatively, the samplecan be treated with a uracil DNA glycosylase (UDG) to hydrolyze theuracil from the DNA.

The method can further comprise conducting a polymerase chain reaction(PCR) to produce labeled-amplicons. In some instances, the polymerasechain reaction is a nested PCR. The nested PCR can comprise conducting afirst PCR comprising mixing the double-stranded labeled-cDNA moleculewith a first PCR mixture comprising a first target specific PCR primer,universal PCR primer, polymerase buffer, DNA polymerase, dNTP mix, orany combination thereof. The first PCR can be conducted in thermalcycler. The first PCR can comprise a thermal cycler program comprising 1cycle of 94° C. for 2 minutes, followed by 30 cycles of 94° C. for 20seconds, 58° C. for 20 seconds, and 68° C. for 20 seconds, followed by 1cycle of 68° C. for 4 minutes and 1 cycle of 4° C. for at least 2minutes. The nested PCR can comprise conducting a second PCR comprisingmixing at least a portion of the amplicons produced in the first PCRreaction with a second PCR mixture comprising a second target specificPCR primer, labeled-universal PCR primer, polymerase buffer, DNApolymerase, dNTP mix, or any combination thereof. The second targetspecific primer can hybridize to a region in the labeled molecule thatis downstream of the first target specific primer. The labeled-universalPCR primer is labeled with a detectable label. In some instances, thelabeled-universal PCR primer is a Cy3-labeled universal PCR primer.Alternatively, the labeled-universal PCR primer is a TYE 563-labeleduniversal PCR primer. The second PCR can be conducted in thermal cycler.The second PCR can comprise a thermal cycler program comprising 1 cycleof 94° C. for 2 minutes, followed by 30 cycles of 94° C. for 20 seconds,58° C. for 20 seconds, and 68° C. for 20 seconds, followed by 1 cycle of68° C. for 4 minutes and 1 cycle of 4° C. for at least 2 minutes. Thesecond PCR of the nested PCR can produce a labeled-amplicon comprisingthe cDNA molecule, oligonucleotide tag and the detectable label. In someinstances, the labeled-cDNA molecule of step 1 c is the labeled-ampliconproduced by the second PCR of the nested PCR.

In some instances, detecting the labeled-cDNA molecule compriseshybridizing at least a portion of the sample comprising thelabeled-amplicons comprising the cDNA molecule, oligonucleotide tag andthe detectable label to a solid support. Hybridizing at least a portionof the sample comprising the labeled-amplicons can comprise ahybridization mixture comprising at least a portion of the samplecomprising the labeled-amplicons produced in the second PCR of nestedPCR, control oligo, hybridization buffer, or any combination thereof.The control oligo can comprise the detectable label conjugated to anoligonucleotide. The detectable label is the same as the detectablelabel in the labeled-amplicon. For example, the labeled-ampliconcomprises a Cy3 label and the control oligo comprises a Cy3-labeledoligonucleotide. The labeled-amplicons in the hybridization mixture aredenatured. In some instances, denaturing the labeled-amplicons comprisesincubating the hybridization mixture at 95° C. In some instances, thehybridization mixture is incubated at 95° C. for at least about 1, 2, 3,4, or 5 minutes. After denaturation of the labeled-amplicons, thehybridization mixture is incubated at 4° C. for at least 2 minutes.Hybridization of the labeled-amplicon to the support can comprise addingat least a portion of the hybridization mixture to the solid support. Insome instances, hybridization of the labeled-amplicon to the solidsupport comprises adding at least a portion of the hybridization mixtureto a well of an AMI array slide. The labeled-amplicon can be hybridizedto the support for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, or48 hours. The labeled-amplicon can be hybridized to the support for atleast about 4 hours. The labeled-amplicon can be hybridized to thesupport overnight. Alternatively, the labeled-amplicon is hybridized tothe support for about 12-14 hours. In other instances, thelabeled-amplicon is hybridized to the support for about 3-5 hours, 4-6hours, 6-8 hours, 8-10 hours, 9-11 hours, 13-15 hours, 14-16 hours,17-19 hours, or 18-20 hours. Hybridization of the labeled-amplicon tothe support can comprise contacting the support with thelabeled-amplicon and incubating the labeled-amplicon and support at ahybridization temperature. In some instances, the hybridizationtemperature is at least about 20° C., 21° C., 22° C., 23° C., 24° C.,25° C., 26° C., 27° C., 28° C., 29° C., 30° C., 32° C., 34° C., 36° C.,38° C., 40° C., 45° C., 50° C., 55° C., 60° C., or 65° C.

The solid support can comprise a plurality of probes. The plurality ofprobes can comprise a sequence that is complementary to at least aportion of the labeled-cDNA molecule or labeled-amplicon. The pluralityof probes can be arranged on the solid support in discrete regions,wherein a discrete region on the solid support comprises probes ofidentical or near-identical sequences. In some instances, two or morediscrete regions on the solid support comprise two different probescomprising sequences complementary to the sequence of two differentunique identifier regions of the oligonucleotide tag.

The method further comprise covering the array slide with an adhesive toproduce a sealed array slide. The sealed array slide can be incubated at37° C. The sealed array slide can be incubated at 37° C. overnight. Insome instances, the sealed array is incubated at 37° C. for at leastabout 12-14 hours. After incubating the sealed array at 37° C., themethod can further comprise removing the sealed array from 37° C. Thehybridization mixture can be removed from each well. The hybridizationmixture can be stored at −20° C. Alternatively, the hybridizationmixture is discarded.

The method can further comprise washing the wells with a first washbuffer. Washing the wells comprises adding a wash buffer to the well andthen aspirating the wash buffer. Additionally, a second wash can beperformed with the same or a second wash buffer. Once the wash buffershave been aspirated from the wells, the array slide can be scanned. Insome instances, the array slide is scanned dry (e.g., fluid is removedfrom the wells). Alternatively, the array slide is scanned wet (e.g.,fluid is in the wells). The array slide can be scanned by a scanner.

The method can comprise fragmentation of the amplification products(e.g., labeled amplicons) to produce fragmented labeled-amplicons. Thefragmented labeled-amplicons can be attached to the solid support. Themethods disclosed herein can further comprise attaching a detectablelabel to the labeled-molecules, labeled-amplicons, or fragmented-labeledamplicons. The detectable label can be attached to thelabeled-molecules, labeled-amplicons, or fragmented-labeled ampliconsprior to attachment of the labeled-molecules, labeled-amplicons, orfragmented-labeled amplicons to the solid support. Alternatively, thedetectable label is attached to the labeled-molecules,labeled-amplicons, or fragmented-labeled amplicons after attachment ofthe labeled-molecules, labeled-amplicons, or fragmented-labeledamplicons to the solid support. The methods disclosed herein cancomprise attaching two or more detectable labels to thelabeled-molecules, labeled-amplicons, or fragmented-labeled amplicons.In some instances, a detectable label is the labeled-cDNA molecule andthe detectable label is incorporated into the labeled-amplicon. Forexample, a Cy3 universal PCR primer is annealed to the labeled-cDNAmolecule. Amplification of the labeled-cDNA molecule with Cy3 universalPCR primer can produce a Cy3-labeled amplicons. The methods disclosedherein can further comprise attaching a second detectable label to thefirst-detectable labeled-molecule. For example, The methods disclosedherein can comprise attaching biotin to the Cy3-labeled amplicons toproduce biotin/Cy3-labeled amplicons.

In some instances, detecting the labeled-cDNA molecule comprises afluorescent reader. The fluorescent reader can be a Sensovation FLAIRinstrument.

In some instances, the data from the scanner is stored on a computer.Alternatively, or additionally, the data from the scanner is exported.In some instances, the data from the scanner is transmittedelectronically. Exportation and/or transmission of the data can compriseone or more computer networks.

Further disclosed herein are methods, kits, and systems forstochastically labeling a molecule. Generally, the method comprisescontacting a sample comprising a plurality of molecules with a pluralityof oligonucleotide tags and randomly attaching one or moreoligonucleotide tags from the plurality of oligonucleotide tags to oneor more molecules in the sample. The plurality of oligonucleotide tagscomprises oligonucleotide tags comprising two or more different uniqueidentifier regions.

In some instances, the methods, kits, and systems compriseconcentrations of the different oligonucleotide tags in the plurality ofoligonucleotide tags. For example, the different oligonucleotide tagsare present in the plurality of oligonucleotide tags in the sameconcentration. Alternatively, the concentration of at least oneoligonucleotide tag in the plurality of oligonucleotide tags is greaterthan the concentration of at least one other oligonucleotide tag in theplurality of oligonucleotide tags. The concentration of the at least oneoligonucleotide tag in the plurality of oligonucleotide tags is at leastabout 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70,80, 90, or 100 times greater than the concentration of the at least oneother oligonucleotide tag in the plurality of oligonucleotide tags. Insome instances, the concentration of at least one oligonucleotide tag inthe plurality of oligonucleotide tags is less than the concentration ofat least one other oligonucleotide tag in the plurality ofoligonucleotide tags. The concentration of the at least oneoligonucleotide tag in the plurality of oligonucleotide tags is at leastabout 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70,80, 90, or 100 times less than the concentration of the at least oneother oligonucleotide tag in the plurality of oligonucleotide tags. Insome instances, at least about 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 100% of the differentoligonucleotide tags in the plurality of oligonucleotide tags arepresent in the plurality of oligonucleotide tags in the same or similarconcentration. Alternatively, at least about 1%, 2%, 3%, 4%, 5%, 10%,15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 100% ofthe different oligonucleotide tags in the plurality of oligonucleotidetags are present in the plurality of oligonucleotide tags in differentconcentrations.

The oligonucleotide tags can further comprise a target specific region,universal primer binding site, or any combination thereof. In someinstances, the unique identifier region is between the target specificregion and the universal primer binding site. The oligonucleotide tagscan be attached to the molecules by hybridization, ligation, or anycombination thereof. In some instances, one or more oligonucleotide tagsare attached to a molecule. The oligonucleotide tag can be attached tothe 5′ end of the molecule, 3′ end of the molecule, an internal sitewithin the molecule, or any combination thereof. One or both ends of theoligonucleotide tag can be attached to the molecule.

The molecule can be a polynucleotide. The polynucleotide can compriseRNA, DNA, or any combination thereof. The molecule can be an RNAmolecule. The RNA molecule can be an mRNA. The molecule can bepolyadenylated. Alternatively, the molecule is not polyadenylated.

Further disclosed herein are digital pre-amplification methods forincreasing the quantity of a nucleic acid molecule in a sample.Generally, the method comprises (a) stochastically labeling a nucleicacid molecule in a sample by any of the methods disclosed herein toproduce a labeled-nucleic acid molecule, wherein the labeled-nucleicacid molecule comprises an oligonucleotide tag attached to the nucleicacid molecule; and (b) amplifying the labeled-nucleic acid molecule toproduce a plurality of labeled-amplicons, wherein a labeled-amplicon inthe plurality of labeled-amplicons is a copy of the labeled-nucleic acidmolecule. The labeled-nucleic acid molecule of step (a) can berepeatedly amplified to increase the quantity of the nucleic acidmolecule in the sample. The oligonucleotide tag comprises a uniqueidentifier region that can be used to distinguish identical or nearlyidentical nucleic acid molecules.

Stochastic labeling of the nucleic acid molecule prior to amplificationcan enable the identification of clonally replicated moleculesoriginating from the sample template parent molecule. Stochasticlabeling of the nucleic acid molecule prior to amplification can allowfor controlled amplification of the nucleic acid molecule, wherein theamplification of an individual nucleic acid molecule can be tracked andmonitored by the oligonucleotide label. The digital pre-amplificationmethod can account for the true abundance levels of nucleic acidmolecules in a sample. This method can be particularly useful forsamples comprising limited quantities of a nucleic acid molecule. Forexample, this method can be used to increase the quantity of a nucleicacid molecule from a single cell. Stochastic labeling of the nucleicacid molecule sin the cell followed by amplification of thelabeled-nucleic acid molecules can allow for more precise quantitativemeasurements of the nucleic acid molecules.

In some instances, the labeled-nucleic acid molecules in the sample areamplified at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times.Alternatively, the labeled-nucleic acid molecules in the sample areamplified at least about 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50,60, 70, 80, 90, or 100 times.

Digital pre-amplification of the nucleic acid molecules can enablerepeated sampling of the nucleic acid molecules in the sample withoutdepletion of the original sample. Repeated sampling of the nucleic acidmolecules in the sample can comprise conducting one or more measurementsand/or experiments on the labeled-amplicons produced from theamplification or repeated amplification reactions conducted on thelabeled-nucleic acid molecules. Repeated sampling of the nucleic acidmolecules in the sample can comprise measurements for detecting and/orquantifying a nucleic acid molecule. Repeated sampling of the nucleicacid molecule in the sample can comprise conducting additionalexperimentation on the nucleic acid molecules in the sample.

In some embodiments, methods, kits, and systems for gene-specificdetection of labeled molecules are disclosed. The methods, kits, andsystems can be used to increase the detection specificity for one ormore genes of interest. A schematic of the method is depicted in FIG. 7.Generally, the method comprises: a) hybridizing at least one targetmolecule to a solid support; and b) hybridizing a labeled gene-specificoligo to the target molecule to produce a labeled-target molecule.

Further disclosed herein are methods, kits and systems for the absolutequantification of one or more molecules. FIG. 17 depicts a comparison ofthe quantification of two genes (gene A and gene B). Quantification ofthe two genes by a standard array readout can provide a relativequantification of genes A and B. In the standard array readout, thegenes are amplified and the amplicons are hybridized to an array. Therelative amounts of genes A and B can be detected by fluorescence andthe intensity (e.g., brightness) of the signal can be used to determinethat the quantity of gene B is greater than the quantity of gene A. Thedigital amplification method disclosed herein can be used to provide anabsolute quantification of genes A and B. The absolute quantificationmethod can comprise (a) stochastically labeling two or more genes with aplurality of oligonucleotide tags to produce a stochastically labeledmolecule, wherein the plurality of oligonucleotide tags comprises two ormore different unique identifier region; (b) amplifying thestochastically labeled molecule to produce one or more stochasticallylabeled amplicons; and (c) detecting the number of different uniqueidentifier regions associated with each stochastically labeledamplicons, thereby determining the absolute quantity of two or moremolecules. As shown in FIG. 17B, detecting the unique identifier regionscomprises hybridizing the stochastically labeled amplicons to a solidsupport (e.g., array). The stochastically labeled amplicons canhybridize to discrete locations on the solid support and the number ofdifferent unique identifier regions can be determined by counting thenumber of discrete locations as detected by fluorescence.

FIG. 19 depicts a schematic of an absolute quantification method of oneor more RNA molecules. As shown in Step 1 of FIG. 19, cDNA synthesis ofone or more target RNA molecules comprises annealing the oligodTsequence (e.g., target specific region, 1920) of an oligonucleotide tag(1920) to the polyA tail of a mRNA molecule (1910). The oligonucleotidetag (1920) further comprises a unique identifier region (1940) and auniversal primer binding site (1950). The unique identifier region(1940) may comprise a predetermined sequence. Alternatively, the uniqueidentifier region (1940) comprises a random sequence. The resulting cDNAmolecule (1960) comprises a copy of the mRNA molecule, the uniqueidentifier region (1940) and the universal primer binding site (1950).As shown in Step 2, the cDNA molecule (1960) can be amplified by nestedPCR comprising a first forward primer (1980), a second forward primer(1990) and a reverse primer comprising universal primer (1970) toproduce one or more labeled amplicons (e.g., amplicons comprising theunique identifier region). The forward primers (1980, 1990) may begene-specific primers. The labeled amplicons can be detected by anymethod known in the art. Absolute quantitation of mRNA molecules canoccur by the detection and counting of different unique identifierregions.

FIG. 20 depicts another method for quantifying one or more molecules.The method may comprise (a) reverse transcribing one or more RNAmolecules using a plurality of oligonucleotide tags (2030) comprisingtwo or more oligonucleotide tags (2020) comprising a target specificregion (2050), a unique identifier region (2060) and a universal primerbinding site (2070) to produce one or more stochastically labeled cDNAcopies, wherein the stochastically labeled cDNA copies comprise theunique identifier region. The unique identifier region may comprise arandom sequence. The method may further comprising amplifying thestochastically labeled cDNA copies to produce one or more stochasticallylabeled amplicons. Amplifying may comprise PCR and T7 amplification. Thestochastically labeled amplicons may comprise the unique identifierregion. The method may further comprise detecting the stochasticallylabeled cDNA copies or stochastically labeled amplicons. Detecting thestochastically labeled molecules can comprise hybridizing thestochastically labeled molecules to one or more digital arrays todetermine the number of distinct labels for each gene of interest.Hybridization may require both the presence of the mRNA sequence, mostlikely a segment on the 3′ exon of the gene, and the unique identifierregion. The array may comprise 7 million features. The one or moremolecules may be in a sample. The sample may comprise 20,000 differentmRNA sequences. The method may comprise determining the number of copiesof each mRNA present in the sample. The plurality of oligonucleotidetags may comprise 350 or more oligonucleotide tags. In some instances, asubset of the 350 oligonucleotide tags may be applied at a lowerconcentration to increase the effective dynamic range of measurement.

FIG. 25 depicts another method of absolute quantitation of mRNAmolecules. As shown in FIG. 25, the method comprises (a) conducting areverse transcription reaction with an oligonucleotide tag (2560) toproduce a stochastically labeled cDNA molecule (2520), wherein thestochastically labeled cDNA molecule comprises a cDNA copy of an mRNAmolecule (2510), a unique identifier region (2540) and a universalprimer binding site (2550); and (b) detecting the stochastically labeledcDNA molecule. The oligonucleotide tag (2560) can serve as a primer forthe reverse transcription reaction. The oligonucleotide tag (2560) maycomprise a target specific region (2530), unique identifier region(2540) and a universal primer binding site (2550). The method mayfurther comprise absolutely quantifying the mRNA molecules based on thedetection of the stochastically labeled cDNA molecules. Detection of thestochastically labeled cDNA molecules may comprise counting the numberof different unique identifier regions that are associated with eachtype of cDNA molecule. The method may further comprise amplifying thestochastically labeled cDNA molecule prior to said detecting to produceone or more stochastically labeled amplicons.

Further disclosed herein are methods, kits and systems for determiningthe DNA copy number. A general schematic of the method is depicted inFIG. 21. As shown in step 1 of FIG. 21, a genomic DNA (2110) can befragmented to produce a DNA fragment (2130). Fragmentation of thegenomic DNA may occur by any method known in the art. For example,fragmentation may comprise mechanical shearing. Alternatively,fragmentation may comprise digestion of the genomic DNA with one or morerestriction nuclease. As shown in Step 2 of FIG. 21, the DNA fragments(2120) can be stochastically labeled with a plurality of oligonucleotidetags (2140) to produce a stochastically labeled molecule (2170). Theoligonucleotide tag (2140) may comprise an adapter sequence (2150) and aunique identifier region (2160). The adapter sequence (2150) may enableattachment of the oligonucleotide tag (2140) to the DNA fragments. Theadapter sequence (2150) may comprise one or more nucleotides that cananneal to the DNA fragments. Each stochastically labeled molecule (2170)may comprise one or more oligonucleotide tags (2150). The method mayfurther comprise amplifying the stochastically labeled molecules (2170)to produce one or more stochastically labeled amplicons. The method mayfurther comprise removing one or more DNA fragments prior toamplification. Removing the one or more DNA fragments may comprisedigesting the DNA fragments with one or more restriction enzymes priorto amplification to prevent the replication of certain fragments. Themethod may further comprise detecting the stochastically labeledmolecules. Detection may comprise hybridization to digital arraysdetects the number of distinct unique identifier regions ligated to eachDNA fragment.

Further disclosed herein are methods, kits and systems for analyzing oneor more RNA molecules. The RNA molecules may be a small RNA molecule.The small RNA molecule may be a microRNA. FIG. 22 depicts a generalmethod for analyzing a small RNA molecule. As shown in Step 1 of FIG.22, one or more miRNA molecules (2210) are stochastically labeled with afirst plurality of oligonucleotide tags (2230). The oligonucleotide tags(2230) may comprise an adapter sequence (2240) and a unique identifierregion (2250). The adapter sequence (2240) may enable attachment of theoligonucleotide tag (2230) to the miRNA molecule (2220) to produce a3′-stochastically labeled miRNA (2260). As shown in Step 2 of FIG. 22,the method may further comprise stochastically labeling the3′-stochastically labeled microRNA (2260) with a second plurality ofoligonucleotide tags (2270). The second plurality of oligonucleotidetags (2270) may comprise an adapter sequence (2290) and a uniqueidentifier region (2280). The adapter sequence (2290) may enableattachment of the oligonucleotide tag (2270) to the 3′-stochasticallylabeled miRNA molecule (2260) to produce a 5′ and 3′-stochasticallylabeled miRNA (2295). The method may further comprise reversetranscribing the stochastically labeled miRNA, amplifying thestochastically labeled miRNA, detecting the stochastically labeledmiRNA, quantifying the miRNA by detecting the stochastically labeledmiRNA, hybridizing the stochastically labeled miRNA to an array, or acombination thereof. The array may be a digital array. The miRNAmolecule may comprise any of the miRNA sequences. For example, the miRNAmolecule may comprise a sequence disclosed in miRBase 18http://www.mirbase.org/, which was released November 2011 and lists 1921unique mature human miRNAs. An array of 2 million features canadequately detect 1000 labels ligated to the 1921 miRNAs.

The methods, kits and systems disclosed herein can be used for geneticaldiagnosis. For example, the methods, kits and systems disclosed hereincan be used for single cell pre-implantation genetic diagnosis (PGD).Primary challenges with single-cell genomic DNA amplification assays canbe from allele dropout and replication bias. As shown in the computationmodeling analysis depicted in FIG. 23A where every molecule has a 0.8probability of replication, molecules of 1:1 initial copy ratios caneasily be distorted to 1:10 or greater just after a few replicationcycles. However, when labels are first attached prior to amplification,counting labels to determine copy number is unaffected by replicationbias, so long as replication occurs. Aneuploidy determination and largeregions of deletion or amplification can be easily and accuratelydetermined by the stochastic labeling method disclosed herein. FIG. 23Bdepicts a schematic of the general method. As shown in Step 1 of FIG.23B, the method may comprise fragmenting a genomic DNA (gDNA, 2310) toproduce one or more fragmented molecules (2320). Fragmentation of thegDNA (2310) may comprise any method known in the art. For example,fragmentation may comprise conducting a restriction digest reaction. Asshown in Step 2 of FIG. 23B, the fragmented DNA (2320) can bestochastically labeled with a plurality of oligonucleotide tags (2380)to produce one or more stochastically labeled molecules (2330). Thestochastically labeled molecule (2330) may comprise one or moreoligonucleotide tags (2380). The oligonucleotide tags (2380) maycomprise unique identifier sequence (2350) and a universal primerbinding site (2340). The stochastically labeled molecule (2380) may beamplified using one or more primers (2360, 2370) that can hybridize tothe universal primer binding site (2340) to produce one or morestochastically labeled amplicons. As shown in Step 3 of FIG. 23B, thestochastically labeled molecules (2330) can be detected by a GeneChipdetector (2395). The stochastically labeled molecule (2330) canhybridize to a probe (2390) on the GeneChip detector (2395).

The methods, kits, and systems disclosed herein can be used in fetaldiagnostics. The method may comprise (a) fragmenting a nucleic acidmolecule in a sample to produce one or more nucleic acid fragments; (b)stochastically labeling the one or more nucleic acid fragments with aplurality of oligonucleotide tags comprising a unique identifier regionto produce one or more stochastically labeled molecules; and (c)detecting the stochastically labeled molecules by counting the number ofunique identifier regions. The method may further comprise diagnosing afetal genetic disorder based on the detection of the stochasticallylabeled molecules.

FIG. 24 depicts a general schematic for using the stochastic labelingmethod in fetal diagnostics. In 100 nanograms of circulating DNA theremay be about 10,000 genome equivalents. the first trimester of maternalplasma, the total concentration of the fetal DNA can be about 10% of thetotal DNA in the maternal plasma sample. The method, as depicted in FIG.24, may comprise fragmenting the DNA molecules (2410). Fragmentation maycomprise the use of a 4-base restriction enzyme cutter. The fragmentedDNA molecules may be stochastically labeled with a plurality ofoligonucleotide tags (2420). Stochastic labeling may comprise ligatingone or more oligonucleotide tags to the fragmented DNA molecules toproduce one or more stochastically labeled molecules. The stochasticallylabeled molecules may be amplified in a multiplex reaction (2430) toproduce one or more stochastically labeled amplicons. The stochasticallylabeled amplicons may be detected on an array (2440). The array maycomprise 5 million features. Diagnosis of a fetal genetic disorder(e.g., trisomy 21) can be based on the detection of the stochasticallylabeled amplicons (2450, 2460). The 100,000 oligonucleotide tags may besynthesized as described in: Methods for screening factorial chemicallibraries, Stephen P. A. Fodor et al, U.S. Pat. No. 5,541,061, issuedJul. 30, 1996.

FIG. 26 depicts a schematic for stochastic labeling of one or moremolecules with an inert primer. The method may comprise (a) reversetranscribing an mRNA molecule (2610) with a primer (2620) comprising anoligodU sequence to produce a cDNA copy of the mRNA molecule (2630),wherein the cDNA copy comprises a 3′ polyA tail and a 5′ oligodTsequence; and (b) stochastically labeling the cDNA copy (2620) with anoligonucleotide tag (2640) comprising a universal primer binding site(2650), unique identifier region (2660) and an oligodU sequence (2670)to produce stochastically labeled cDNA molecule (2680). The method mayfurther comprise a second stochastic labeling step to produce astochastically labeled cDNA molecule, wherein both ends of the cDNAmolecule are stochastically labeled with an oligonucleotide tag. Themethod may further comprise treating the sample with uracil DNAglycosylase (UDG) to remove the oligodU primer (2620) and theoligonucleotide tags comprising the oligodU sequence. The method mayfurther comprise amplifying the stochastically labeled cDNA molecule toproduce one or more stochastically labeled amplicons.

FIG. 27 depicts a schematic for analyzing one or more molecules. Themethod may comprise (a) reverse transcribing an mRNA molecule (2710)with an oligonucleotide tag (2720) comprising an oligodU sequence(2730), unique identifier region (2740), and a universal primer bindingsite (2750) to produce a cDNA copy (2760) of the mRNA molecule, whereinthe cDNA copy (2760) comprises the unique identifier region (2740) andthe universal primer binding site (2750); and (b) amplifying the cDNAcopy with a first primer (2790) comprising an oligodU sequence and asecond primer (2780) comprising the universal primer sequence to producestochastically labeled amplicons. The method may comprise treating themolecules with one or more restriction enzymes. The method may furthercomprise conducting an emulsion PCR reaction on the stochasticallylabeled molecules.

The methods depicted in FIG. 26-27 may rely on homopolymer tailing. FIG.28 depicts a method that does not rely on homopolymer tailing. Asdepicted in FIG. 28, the method may comprise reverse transcribing anmRNA molecule to produce a cDNA copy. Reverse transcription of the mRNAmolecule may be carried out on a bead surface. The method may compriseRNAse H digestion of the mRNA molecule. The method may comprisestochastically labeling the cDNA copy with a plurality ofoligonucleotide tags to produce one or more stochastically labeled cDNAmolecules. The oligonucleotide tag may comprise a secondary structure.The secondary structure may be a hairpin. The oligonucleotide tag maycomprise a universal primer binding site, unique identifier region,restriction enzyme recognition site, target specific region, or anycombination thereof. The loop portion of the hairpin oligonucleotide tagmay comprise a universal primer binding sequence. The loop portion ofthe hairpin oligonucleotide tag may comprise a unique identifier region.The loop portion of the hairpin oligonucleotide tag may further comprisea restriction enzyme recognition site. The oligonucleotide tag may besingle stranded. The oligonucleotide tag may be double stranded. Themethod may further comprise amplifying the stochastically labeled cDNAmolecule to produce one or more stochastically labeled amplicons. Themethod may further comprise digesting the stochastically labeledamplicons with a restriction nuclease to produce a digestedstochastically labeled amplicon. The method may further compriseligating one or more primers to the digested stochastically labeledamplicon to produce a primer-stochastically labeled amplicon. The primermay be a sequencing primer. The method may further comprise sequencingthe primer-stochastically labeled amplicon. This method may reduce orprevent un-intended incorporation of oligonucleotide tags during PCRamplification. This method may improve sequencing of the stochasticallylabeled molecules compared to the sequencing of the stochasticallylabeled molecules from a reaction based on homopolymer tails. Thismethod may reduce or prevent sequencing errors. The oligonucleotide tagmay comprise a 3′ phosphate. The 3′ phosphate can prevent extension ofthe 3′ end during a PCR reaction, thereby reducing or preventingnon-specific amplification.

FIG. 29 depicts a linear amplification method. The method may comprisereverse transcribing one or more mRNA molecules by stochasticallylabeling the one or more RNA molecules with a plurality ofoligonucleotide tags to produce one or more cDNA copies of the mRNAmolecules, wherein the cDNA copies comprise the oligonucleotide tag. Theoligonucleotide tag may comprise a universal primer binding site, uniqueidentifier region and an oligodT sequence. The method may furthercomprise synthesizing a DNA copy of the mRNA molecule by second strandsynthesis. The method may comprise linear amplification of thestochastically labeled cDNA molecule. Linear amplification may compriseamplifying the stochastically labeled cDNA molecule by T7 RNApolymerase, nicking enzyme strand displacement synthesis or RiboSPIA(NuGEN). The method may further comprise attaching one or moresequencing primes to the stochastically labeled molecule. The method mayfurther comprise amplifying the stochastically labeled molecule toproduce one or more stochastically labeled amplicons. The method mayfurther comprise sequencing the stochastically labeled amplicons. Thismethod may comprise a low level of initial amplification followed byexponential PCR. This method may be independent of ligation. This methodmay reduce or prevent artifacts generated by PCR.

FIG. 30 depicts a method of stochastically labeling one or moremolecules by strand switching. The method may comprise reversetranscribing a first strand synthesis in the presence of a strand-switcholigonucleotide to produce a stochastically labeled cDNA molecule. Themethod may further comprise amplifying the stochastically labeled cDNAmolecule.

FIG. 31 depicts a method of stochastically labeling one or moremolecules by random priming. The method may comprise reversetranscribing an mRNA molecule to produce a stochastically labeled cDNAcopy. Reverse transcribing may comprise stochastically labeling one ormore molecules with a plurality of oligonucleotide tags, wherein theoligonucleotide tag comprises an oligodU sequence, a unique identifiersequence and a universal primer sequence. The oligonucleotide tag mayfurther comprise a restriction enzyme recognition site. The method mayfurther comprise removing the mRNA molecules with RNAse H. The methodmay further comprise conducting a second strand synthesis reaction witha second set of oligonucleotide tags. The second set of oligonucleotidetags may comprise a universal primer binding site, a restriction enzymerecognition site, and a unique identifier region. The method may furthercomprise treating the sample with UDG to remove oligonucleotide tagscomprising one or more uracils. The method may further compriseamplifying the stochastically labeled molecules. The method may furthercomprise attaching one or more adapters to the stochastically labeledmolecules. The oligonucleotide tag may comprise any three nucleotides(e.g., C, G, T—no A; C, G, A—no T). The oligonucleotide tag may compriseany two nucleotides (e.g., G, T—no A, C; A, C—no G, T). As shown in FIG.31, the method may comprise first strand cDNA synthesis with an-oligo dT(or dU for subsequent removal with UDG) oligonucleotide tag bearing 12variable label nucleotides (C/G/T—A was excluded to prevent spuriousself-priming to the T/U string). However, instead of TdT tailing togenerate the second PCR priming site, an oligonucleotide tag containinga quasi-random string and a PCR sequence is used.

FIG. 43 depicts a schematic of a method for absolute quantitation of oneor more molecules directly from one or more cell lysates. As shown inFIG. 43, an intact cell (4310) comprising one or more DNA molecules(4320), RNA molecules (4330), proteins (4340), or a combination thereofis lysed to produce a lysed cell (4350). The one or more DNA molecules(4320), RNA molecules (4330) and/or proteins (4340) can be released fromthe cell. The quantity of one or more mRNA molecules (4330) can bedetermined by stochastically labeling the mRNA molecules with aplurality of oligonucleotide tags (4390). The oligonucleotide tag maycomprise a target specific region (4360), unique identifier region(4370) and a universal primer binding site (4380).

In some instances, the target molecule is a DNA molecule. Alternatively,the target molecule is an RNA molecule. In some instances, the methodsdisclosed herein further comprise reverse transcribing the RNA molecule.The labeled gene-specific oligo can comprise one or more nucleotides.The one or more nucleotides can be a deoxynucleotide. Alternatively, oradditionally, the one or more nucleotides are a deoxyribonucleotide. Theone or more nucleotides can be a synthetic nucleotide. The labeledgene-specific oligo can comprise at least about 5 nucleotides.Alternatively, the labeled gene-specific oligo comprises at least about10 nucleotides. Alternatively, the labeled gene-specific oligo comprisesat least about 12 nucleotides. The labeled gene-specific oligo cancomprise at least about 15 nucleotides. The labeled gene-specific oligocan comprise at least about 17 nucleotides. The labeled gene-specificoligo can comprise at least about 20 nucleotides. In some instances, thelabeled gene-specific oligo comprises at least about 25, 30, 35, 40, 45,50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides.

The labeled gene-specific oligo can comprise a target specific region.The target specific region of the labeled gene-specific oligo can be atleast partially complementary to at least a portion of the targetmolecule. In some instances, the target specific region comprises atleast about 5 nucleotides that are complementary to at least a portionof the target molecule. Alternatively, the target specific regioncomprises at least about 10 nucleotides that are complementary to atleast a portion of the target molecule. In other instances, the targetspecific region comprises at least about 12 nucleotides that arecomplementary to at least a portion of the target molecule. The targetspecific region can comprise at least about 15 nucleotides that arecomplementary to at least a portion of the target molecule. The targetspecific region can comprise at least about 17 nucleotides that arecomplementary to at least a portion of the target molecule. The targetspecific region can comprise at least about 20 nucleotides that arecomplementary to at least a portion of the target molecule. The targetspecific region can comprise at least about 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 96, or 100 nucleotides that arecomplementary to at least a portion of the target molecule. The targetspecific region can comprise a sequence that is at least about 60%complementary to at least a portion of the target molecule.Alternatively, the target specific region comprises a sequence that isat least about 70% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 80% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 85% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 90% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 95% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 97% complementary to at least a portion of the targetmolecule. The target specific region can comprise a sequence that is atleast about 98% complementary to at least a portion of the targetmolecule.

The labeled gene-specific oligo can comprise any label disclosed herein.In some instances, the label is a fluorophore. Alternatively, the labelis a cyanine dye (e.g., Cy3, Cy5).

The solid support can be any solid support disclosed herein. In someinstances, the solid support is a detector array. The detector array cancomprise a plurality of probes. The target molecule can be hybridized toone or more probes of the plurality of probes on the detector array.

The method can further comprise amplifying the target molecule prior tohybridization to the solid support. The methods disclosed herein canfurther comprise sequencing the target molecules hybridized to the solidsupport. The methods disclosed herein can be used to preventfalse-positive detection of PCR amplified DNAs that do not contain thegene of interest.

The method can further comprise detecting the labeled-target molecules.Methods to detect the labeled-target molecule can comprise any of thedetection methods and instruments disclosed herein. In some instances,detecting the labeled-target molecule comprises detecting the label.Detecting the labeled-target molecule can comprise a fluorometer.Alternatively, detecting the labeled-target molecule comprises aluminometer. In other instances, detecting the labeled-target moleculecomprises a plate reader.

Further disclosed herein are methods, kits, and systems for capturingand/or enriching a population of target molecules. FIG. 8 shows aschematic of the method. Generally, the method comprises: a)stochastically labeling one or more nucleic acid molecules in a sampleto produce a stochastically labeled molecule; and b) capturing one ormore stochastically labeled molecules to produce a captured molecule,wherein the captured molecule comprise a target molecule.

Capturing the stochastically labeled molecule can comprise the use ofone or more gene-specific oligos. The gene-specific oligos can attach toa specific stochastically labeled molecule to produce an oligo linkedmolecule. In some instances, the methods disclosed herein furthercomprise isolating the oligo linked molecule from the sample. Thegene-specific oligo can comprise a label or tag. The label or tag canenable isolation of the oligo linked molecule.

Alternatively, capturing the stochastically labeled molecule cancomprise contacting the sample comprising the stochastically labeledmolecules with a solid support. In some instances, the stochasticallylabeled molecule comprising the target molecule hybridizes to the solidsupport, thereby capturing the stochastically labeled molecule.Alternatively, the stochastically labeled molecule hybridized to thesolid support does not comprise the target molecule and capturing thestochastically labeled molecule comprises collecting any unboundstochastically labeled molecules (e.g., stochastically labeled moleculesthat are not hybridized to the solid support). The solid support can beany of the solid supports disclosed herein. In some instances, the solidsupport is an array. In other instances, the solid support is a bead.The bead can be a magnetic bead. In some instances, capturing thestochastically labeled molecule comprises the use of a magnet.

The method can further comprise amplification of the stochasticallylabeled molecule and/or captured molecule. Amplification of thestochastically labeled molecule and/or captured molecule can compriseany of the amplification methods disclosed herein. In some instances,amplification of the stochastically labeled molecule and/or capturedmolecule comprises PCR.

The methods disclosed herein can further comprise sequencing of thecaptured molecule. Sequencing can comprise any of the sequencing methodsdisclosed herein. In some instances, the captured molecules are directlysequenced on the solid support.

Further disclosed herein are methods, kits, and systems for digitaldetection and/or quantification of a nucleic acid molecule. Generally,the methods, kits, and systems comprise (a) stochastically labeling anucleic acid molecule with a plurality of oligonucleotide tags toproduce a stochastically labeled-nucleic acid molecule; and (b)detecting and/or quantifying the stochastically labeled-nucleic acidmolecule. The nucleic acid molecule can be a DNA molecule. The nucleicacid molecule can be from a cell. Alternatively, the nucleic acidmolecule is a cell-free molecule. The nucleic acid molecule can bederived from a subject. Alternatively, the nucleic acid molecule can bederived from a foreign subject. The foreign subject can be a pathogen(e.g., virus, bacteria, fungus).

The method can further comprise amplifying the stochasticallylabeled-nucleic acid molecules to produce stochastically-labeled nucleicacid molecule amplicons. The stochastically labeled-nucleic acidmolecules or any products thereof (e.g., stochastically-labeled nucleicacid molecule amplicons) can be repeatedly amplified.

In some instances, the method further comprises attaching one or moredetectable labels to the stochastically labeled-nucleic acid moleculesor products thereof. In some instances, at least one detectable label isattached to the stochastically labeled-nucleic acid molecules orproducts thereof. Alternatively, at least two detectable labels areattached to the stochastically labeled-nucleic acid molecules orproducts thereof. The detectable label can be biotin. Alternatively, thedetectable label is a fluorescent dye. The fluorescent dye can be a Cy™dye or a TYE 563 dye. The Cy™ dye can be Cy3.

The method can further comprise hybridization of the stochasticallylabeled-nucleic acid molecules or any products thereof to a solidsupport. The solid support can be a bead. Alternatively, the solidsupport is an array.

The method can further comprise conducting a sequencing reaction todetermine the sequence of at least a portion of the stochasticallylabeled-nucleic acid molecule or product thereof. In some instances, atleast a portion of the oligonucleotide tag of the stochasticallylabeled-nucleic acid molecule or product thereof is sequences. Forexample, at least a portion of the unique identifier region of theoligonucleotide tag is sequenced. In another example, at least a portionof the target specific region of the oligonucleotide tag is sequenced.Alternatively, or additionally, at least a portion of the nucleic acidmolecule of the stochastically labeled-nucleic acid molecule issequenced.

Detection and/or quantification of the stochastically labeled-nucleicacid molecules can comprise detection and/or quantification of thestochastically-labeled cDNA copies and/or the stochastically-labelednucleic acid molecule amplicons. Detection and/or quantification of thestochastically labeled-nucleic acid molecules can further comprisedetection of one or more detectable labels attached to thestochastically labeled-nucleic acid molecules or products thereof.Detection and/or quantification of the stochastically labeled-nucleicacid molecules or products thereof can comprise any of the detectionand/or quantification methods disclosed herein. For example, afluorescence reader can be used to detect and/or quantify thestochastically labeled-nucleic acid molecules or products thereof.Alternatively, a microarray reader can be used to detect and/or quantifythe stochastically labeled-nucleic acid molecules or products thereof.

Further disclosed herein are methods, kits, and systems for digitaldetection and/or digital quantification of viral molecules. Generally,the methods, kits, and systems comprise (a) stochastically labeling oneor more viral molecules with a plurality of oligonucleotide tags toproduce a stochastically labeled-viral molecule; and (b) detectingand/or quantifying the stochastically labeled-viral molecule. In someinstances, the viral molecules are nucleic acid molecules. The nucleicacid molecules can be DNA or RNA.

The method can further comprise conducting a reverse transcriptionreaction to produce a stochastically-labeled cDNA copy of thestochastically-labeled viral molecule (e.g., stochastically-labeledviral RNA molecule). The stochastically-labeled viral molecule can berepeatedly reverse transcribed to produce multiplestochastically-labeled cDNA copies of the stochastically-labeled viralmolecule. The methods can further comprise amplifying the stochasticallylabeled-viral molecules or any products thereof (e.g.,stochastically-labeled cDNA copy) to produce stochastically-labeledviral amplicons. The stochastically labeled-viral molecules can berepeatedly amplified. Alternatively, the products of thestochastically-labeled viral molecules can be repeatedly amplified. Insome instances, the products of the stochastically-labeled viralmolecules are the stochastically-labeled cDNA copies of thestochastically-labeled viral molecule. Alternatively, the products ofthe stochastically-labeled viral molecules are thestochastically-labeled viral amplicons.

In some instances, the method further comprises attaching one or moredetectable labels to the stochastically labeled-viral molecules orproducts thereof. In some instances, at least one detectable label isattached to the stochastically labeled-viral molecules or productsthereof. Alternatively, at least two detectable labels are attached tothe stochastically labeled-viral molecules or products thereof. Thedetectable label can be biotin. Alternatively, the detectable label is afluorescent dye. The fluorescent dye can be a Cy™ dye or a TYE 563 dye.The Cy™ dye can be Cy3.

The method can further comprise hybridization of the stochasticallylabeled-viral molecules or any products thereof to a solid support. Thesolid support can be a bead. Alternatively, the solid support is anarray.

The method can further comprise conducting a sequencing reaction todetermine the sequence of at least a portion of the stochasticallylabeled-viral molecule or product thereof. In some instances, at least aportion of the oligonucleotide tag of the stochastically labeled-viralmolecule or product thereof is sequences. For example, at least aportion of the unique identifier region of the oligonucleotide tag issequenced. In another example, at least a portion of the target specificregion of the oligonucleotide tag is sequenced. Alternatively, oradditionally, at least a portion of the viral molecule of thestochastically labeled-viral molecule is sequenced.

Detection and/or quantification of the stochastically labeled-viralmolecules can comprise detection and/or quantification of thestochastically-labeled cDNA copies and/or the stochastically-labeledviral amplicons. Detection and/or quantification of the stochasticallylabeled-viral molecules can further comprise detection of one or moredetectable labels attached to the stochastically labeled-viral moleculesor products thereof. Detection and/or quantification of thestochastically labeled-viral molecules or products thereof can compriseany of the detection and/or quantification methods disclosed herein. Forexample, a fluorescence reader can be used to detect and/or quantify thestochastically labeled-viral molecules or products thereof.Alternatively, a microarray reader can be used to detect and/or quantifythe stochastically labeled-viral molecules or products thereof.

In some instances, digital detection and/or digital quantification ofthe viral molecules can be used to determine the viral load in a subjectsuffering from a viral infection. Alternatively, digital detectionand/or digital quantification of the viral molecules can be used in thediagnosis and/or prognosis of a viral infection. In some instances,digital detection and/or digital quantification of the viral moleculescan be used in monitoring an antiviral therapeutic regimen.

Further disclosed herein are methods, kits, and systems for digitaldetection and/or quantification of a biomarker. The methods, kits, andsystems can be used to quantify a biomarker. Generally, the methods,kits, and systems comprise (a) stochastically labeling a biomarker witha plurality of oligonucleotide tags to produce a stochasticallylabeled-biomarker; and (b) detecting and/or quantifying thestochastically labeled-biomarker. The biomarker can be a cancerbiomarker. The biomarker can be a nucleic acid molecule or a protein.The nucleic acid molecule can be a DNA molecule. Alternatively, thenucleic acid molecule can be a RNA molecule. The biomarker can bederived from a subject. Alternatively, the biomarker can be derived froma foreign subject. The foreign subject can be a pathogen (e.g., virus,bacteria, fungus).

The method can further comprise conducting a reverse transcriptionreaction to produce a stochastically-labeled cDNA copy of thestochastically-labeled biomarker (e.g., stochastically-labeled biomarkerRNA molecule). The stochastically-labeled biomarker can be repeatedlyreverse transcribed to produce multiple stochastically-labeled cDNAcopies of the stochastically-labeled biomarker. The methods can furthercomprise amplifying the stochastically labeled-biomarkers or anyproducts thereof (e.g., stochastically-labeled cDNA copy) to producestochastically-labeled biomarker amplicons. The stochasticallylabeled-biomarkers can be repeatedly amplified. Alternatively, theproducts of the stochastically-labeled biomarkers can be repeatedlyamplified. In some instances, the products of the stochastically-labeledbiomarkers are the stochastically-labeled cDNA copies of thestochastically-labeled biomarker. Alternatively, the products of thestochastically-labeled biomarkers are the stochastically-labeledbiomarker amplicons.

In some instances, the method further comprises attaching one or moredetectable labels to the stochastically labeled-biomarkers or productsthereof. In some instances, at least one detectable label is attached tothe stochastically labeled-biomarkers or products thereof.Alternatively, at least two detectable labels are attached to thestochastically labeled-biomarkers or products thereof. The detectablelabel can be biotin. Alternatively, the detectable label is afluorescent dye. The fluorescent dye can be a Cy™ dye or a TYE 563 dye.The Cy™ dye can be Cy3.

The method can further comprise hybridization of the stochasticallylabeled-biomarkers or any products thereof to a solid support. The solidsupport can be a bead. Alternatively, the solid support is an array.

The method can further comprise conducting a sequencing reaction todetermine the sequence of at least a portion of the stochasticallylabeled-biomarker or product thereof. In some instances, at least aportion of the oligonucleotide tag of the stochasticallylabeled-biomarker or product thereof is sequences. For example, at leasta portion of the unique identifier region of the oligonucleotide tag issequenced. In another example, at least a portion of the target specificregion of the oligonucleotide tag is sequenced. Alternatively, oradditionally, at least a portion of the biomarker of the stochasticallylabeled-biomarker is sequenced.

Detection and/or quantification of the stochastically labeled-biomarkerscan comprise detection and/or quantification of thestochastically-labeled cDNA copies and/or the stochastically-labeledbiomarker amplicons. Detection and/or quantification of thestochastically labeled-biomarkers can further comprise detection of oneor more detectable labels attached to the stochasticallylabeled-biomarkers or products thereof. Detection and/or quantificationof the stochastically labeled-biomarkers or products thereof cancomprise any of the detection and/or quantification methods disclosedherein. For example, a fluorescence reader can be used to detect and/orquantify the stochastically labeled-biomarkers or products thereof.Alternatively, a microarray reader can be used to detect and/or quantifythe stochastically labeled-biomarkers or products thereof.

In some instances, digital detection and/or digital quantification ofthe biomarkers can be used to diagnose or prognose a condition in asubject in need thereof. In some instances, digital detection and/ordigital quantification of the biomarkers can be used to monitor atherapeutic regimen.

The condition can be a cancer. The cancer can be a sarcoma, carcinoma,leukemia, or lymphoma.

Alternatively, the condition is a pathogenic infection. The pathogenicinfection can be a bacterial or viral infection.

Further disclosed herein are methods, kits and systems for counting ordetermining a number of nucleic acid molecules in a sample. The methodmay comprise: (a) providing a plurality of oligonucleotide tags whereina oligonucleotide tag comprises a unique identifier sequence, a targetsequence, and an optional PCR primer sequence; (b) combining a samplecomprising nucleic acid molecules with the plurality of labeled primersto form a labeled nucleic acid molecule, wherein each target nucleicacid molecule is capable of attaching to a oligonucleotide tag with aunique identifier sequence; and (c) detecting (i) the nucleic acidmolecule, a complement of the nucleic acid molecule, a reversecomplement of the nucleic acid molecule, or a portion thereof, and (ii)the oligonucleotide tag, a complement of the oligonucleotide tag, areverse complement of the oligonucleotide tag, or a portion thereof todetermine the count or number of different labeled nucleic acidmolecules, thereby counting or determining a number of nucleic acidmolecules in the sample. The method may comprise counting or determininga number of 10 or more different nucleic acid molecules. The method maycomprise counting or determining a number of 20 or more differentnucleic acid molecules. The different nucleic acid molecules may differby 1 or more nucleotides or base pairs. The different nucleic acids maybe counted simultaneously. Alternatively, the different nucleic acidmolecules may be counted sequentially.

The method of counting or determining a number of nucleic acid moleculesin a sample may comprise: (a) providing a plurality of oligonucleotidetags wherein a oligonucleotide tag comprises a unique identifiersequence, a target sequence, and an optional PCR primer sequence; (b)combining a sample comprising nucleic acid molecules with the pluralityof labeled primers to form a labeled nucleic acid molecule, wherein theattachment of the nucleic acid molecule to the oligonucleotide tag formsa unique molecule-tag junction; and (c) detecting the uniquemolecule-tag junction, a complement of the unique molecule-tag junction,a reverse complement of the unique molecule-tag junction, or a portionthereof to determine the count or number of different labeled nucleicacid molecules, thereby counting or determining a number of nucleic acidmolecules in the sample. The method may comprise counting or determininga number of 10 or more different nucleic acid molecules. The method maycomprise counting or determining a number of 20 or more differentnucleic acid molecules. The different nucleic acid molecules may differby 1 or more nucleotides or base pairs. The different nucleic acids maybe counted simultaneously. Alternatively, the different nucleic acidmolecules may be counted sequentially.

The method of counting or determining a number of nucleic acid moleculesin a sample may comprise: (a) providing a plurality of oligonucleotidetags, wherein the oligonucleotide tag comprises a target-specificsequence, a unique identifier sequence comprising a ribonucleic acid,and an optional PCR primer sequence; (b) combining a sample comprisingnucleic acid molecules with the plurality of oligonucleotide tags toform a labeled nucleic acid molecule, wherein a target nucleic acidmolecule is capable of attaching to oligonucleotide tags with differentunique identifier sequences; (c) synthesizing a copy of the labelednucleic acid molecule, wherein the copy of the labeled nucleic acidmolecule comprises a copy of the nucleic acid molecule and a copy of theoligonucleotide tag and the ribonucleic acid of the unique identifiersequence comprises replaced with a deoxyribonucleic acid; and (d)detecting the copy of the labeled nucleic acid molecule, a complement ofthe copy of the labeled nucleic acid molecule, a reverse complement ofthe copy of the labeled nucleic acid molecule, or a portion thereof todetermine a count of the copy of the labeled nucleic acid molecule,thereby counting or determining a number of nucleic acid molecules inthe sample. The method may comprise counting or determining a number of10 or more different nucleic acid molecules. The method may comprisecounting or determining a number of 20 or more different nucleic acidmolecules. The different nucleic acid molecules may differ by 1 or morenucleotides or base pairs. The different nucleic acids may be countedsimultaneously. Alternatively, the different nucleic acid molecules maybe counted sequentially.

The method of counting or determining a number of RNA molecules in asample may comprise: (a) combining a sample comprising RNA moleculeswith a plurality of oligonucleotide tags, wherein the oligonucleotidetag comprises an RNA-specific sequence, a unique identifier sequence,and an optional PCR primer sequence; (b) synthesizing a copy of an RNAmolecule by attaching a oligonucleotide tag to the RNA molecule to forma labeled DNA molecule, wherein each RNA molecule is capable ofattaching to oligonucleotide tags with different unique identifiersequences and each labeled DNA molecule comprises a copy of the RNAmolecule and a copy of the oligonucleotide tag; and (c) detecting thelabeled DNA molecule, a complement of the labeled DNA molecule, areverse complement of the labeled DNA molecule, or a portion thereof todetermine a count of the labeled DNA molecule, thereby counting ordetermining a number of RNA molecules in the sample.

The method of counting or determining a number of RNA molecules in asample may comprise: (a) providing a plurality of oligonucleotide tags,wherein the oligonucleotide tag comprises an RNA-specific sequence, aunique identifier sequence comprising a ribonucleic acid, and anoptional PCR primer sequence; (b) combining a sample comprising RNAmolecules with the plurality of oligonucleotide tags to form a labeledRNA molecule, wherein a target RNA molecule is capable of attaching tooligonucleotide tags with different unique identifier sequences; (c)synthesizing a copy of the labeled RNA molecule to form a labeled DNAmolecule, wherein the labeled DNA molecule comprises a copy of the RNAmolecule and a copy of the oligonucleotide tag and the ribonucleic acidof the unique identifier sequence comprises replaced with adeoxyribonucleic acid; and (d) detecting the labeled DNA molecule, acomplement of the labeled DNA molecule, a reverse complement of thelabeled DNA molecule, or a portion thereof to determine a count of thelabeled DNA molecule, thereby counting or determining a number of RNAmolecules in the sample.

The method of counting or determining a number of RNA molecules in asample may comprise: (a) combining a sample comprising RNA moleculeswith a plurality of oligonucleotide tags to form a labeled RNA molecule,wherein each target RNA molecule is capable of attaching to a differentlabel; (b) optionally attaching a second oligonucleotide tag to thelabeled RNA molecule to form a dual-labeled RNA molecule; (c)synthesizing a copy of the labeled RNA molecule or dual-labeled RNAmolecule to form a labeled DNA molecule or dual-labeled DNA molecule,wherein the labeled DNA molecule and the dual-labeled DNA moleculecomprise a copy of the oligonucleotide tag and a copy of the RNAmolecule; and (d) detecting the labeled DNA molecule, a complement ofthe labeled DNA molecule, a reverse complement of the labeled-DNAmolecule, the dual-labeled DNA molecule, a complement of thedual-labeled DNA molecule, a reverse complement of the dual-labeled DNAmolecule, or a portion thereof to count or determine the number ofdifferent labeled DNA molecules or different dual-labeled DNA molecules,thereby counting or determining a number of RNA molecules in the sample.

The method of counting or determining a number of RNA molecules in asample may comprise: (a) combining a sample comprising RNA moleculeswith a plurality of labels to form a labeled RNA molecule, wherein eachtarget RNA molecule is capable of attaching to a different label; (b)optionally attaching a second label to the labeled RNA molecule to forma dual-labeled RNA molecule; and (c) detecting the labeled RNA molecule,a complement of the labeled RNA molecule, a reverse complement of thelabeled-RNA molecule, the dual-labeled RNA molecule, a complement of thedual-labeled RNA molecule, a reverse complement of the dual-labeled RNAmolecule, or a portion thereof to count or determine the number ofdifferent labeled RNA molecules or different dual-labeled RNA molecules,thereby counting or determining a number of RNA molecules in the sample.

The method of counting or determining a number of mRNA molecules in asample may comprise: (a) providing a plurality of oligonucleotide tags,wherein the oligonucleotide tag comprises a target-specific sequence, aunique identifier sequence, and an optional PCR primer sequence; (b)combining a sample comprising mRNA molecules with the plurality ofoligonucleotide tags to form a labeled mRNA molecule, wherein eachtarget mRNA molecule is capable of attaching to a differentoligonucleotide tag; (b) synthesizing a copy of the labeled mRNAmolecule to form a labeled DNA molecule, wherein the labeled DNAmolecule comprises a copy of the mRNA molecule and a oligonucleotide tagor a copy of the oligonucleotide tag; and (c) detecting the labeled DNAmolecule, a complement of the labeled DNA molecule, a reverse complementof the labeled DNA molecule, or a portion thereof to determine a countof different labeled DNA molecules, thereby counting or determining anumber of mRNA molecules in the sample.

In one aspect, polyadenylated RNA from a single cell is analyzed by themethods disclosed herein. After cell lysis the polyA RNA may be enrichedby capture on a solid support, such as a bead, having oligo dT attachedor the amplification can be performed on the lysate. A labeled-cDNA copyof the RNA is made by hybridizing a primer that has an oligo dT regionand a label-tag region. The label-tag region being 5′ of the oligo dTregion. Preferably there is an amplification sequence that is 5′ of thelabel-tag region so that the label-tag region, which is variable betweenprimers, is between a 5′ common amplification primer sequence and a 3′oligo dT region. Second strand cDNA is then synthesized using standardmethods, for example use of RNaseH and DNA polymerase. The resultingdsDNA can then be linearly amplified depending on the amplificationprimer sequence. For example, if the amplification primer sequence is aT7 RNA polymerase promoter sequence, antisense RNA can be generated byIVT using T7 RNA pol. If the amplification prime sequence includes asite for s nicking enzyme (e.g. Nt. BspQl), nicking enzyme stranddisplacement can be used to generate DNA copies of the RNA targets. Thecopies can then be modified to include sequencing primers at one or bothends and the products can be sequenced. Sequence information iscollected for the tag and enough of the adjacent sequence to provide anidentification of the target.

In some instances, the oligonucleotide tag comprises a ribonucleic acid.The oligonucleotide tag may comprise a ribonucleic acid that is uracil.The oligonucleotide tag may comprise a ribonucleic acid that iscytosine. The oligonucleotide tag may comprise a ribonucleic acid thatis adenine. The oligonucleotide tag may comprise a ribonucleic acid thatis guanosine.

The unique identifier sequence may comprise a predetermined sequence.The unique identifier sequence may comprise a random sequence.

The target-specific sequence of the oligonucleotide tag may be specificfor a plurality of targets. In some aspects, the target-specificsequence of the oligonucleotide tag comprises an oligo dT sequence. Insome aspects, the target-specific sequence of the oligonucleotide tagmay comprise an oligo dU sequence. In some instances, thetarget-specific sequence does not comprise an oligo dT nor oligo dUsequence.

The copy of the labeled DNA molecule may be synthesized by a reversetranscriptase enzyme. The reverse transcriptase enzyme may be selectedfrom a retroviral reverse transcriptase, a phage DNA polymerase, or aDNA polymerase.

The method may further comprise synthesizing a copy of the labelednucleic acid molecule to replace a ribonucleic acid with adeoxyribonucleic acid.

In some aspects, the detecting step comprises detecting the copy of thelabeled nucleic acid molecule, a complement of the copy of the labelednucleic acid molecule, a reverse complement of the copy of the labelednucleic acid molecule, or a portion thereof. In some aspects, thedetection step may comprise hybridization of the nucleic acid moleculeportion of the labeled nucleic acid molecule, a complement of thenucleic acid molecule portion of the labeled nucleic acid molecule, areverse complement of the nucleic acid molecule portion of the labelednucleic acid molecule, the oligonucleotide tag of the labeled nucleicacid molecule, a complement of the oligonucleotide tag of the labelednucleic acid molecule, a reverse complement of the oligonucleotide tagof the labeled nucleic acid molecule, a portion thereof, or anycombination thereof to a solid support. In some aspects, the detectionstep may comprise hybridization of the nucleic acid molecule portion ofthe copy of the labeled nucleic acid molecule, the oligonucleotide tagportion of the copy of the labeled nucleic acid molecule, a complementthereof, a reverse complement thereof, a portion thereof, or anycombination thereof to a solid support.

In some aspects, the detecting step comprises detecting the copy of theoligonucleotide tag, a complement of the copy of the oligonucleotidetag, a reverse complement of the copy of the oligonucleotide tag, or aportion thereof.

The detection step may comprise hybridization of the unique molecule-tagjunction, a complement of the unique molecule-tag junction, a reversecomplement of the unique molecule-tag junction, or a portion thereof toa solid support. The detection step may comprise hybridization of a copyof the unique molecule-tag junction, a complement of the copy of theunique molecule-tag junction, a reverse complement of the copy of theunique molecule-tag junction, or a portion thereof to a solid support.

In some aspects, the solid support comprises an array. The array maycomprise probes attached to the surface. The array may further comprisea probe feature for each possible labeled nucleic acid moleculecombination. In another aspect, the solid support may comprise a bead.

In some aspects, the detection step comprises sequencing of (i) thenucleic acid molecule portion of the labeled nucleic acid molecule, acomplement thereof, a reverse complement thereof, or a portion thereof,and (ii) the oligonucleotide tag portion of the labeled nucleic acidmolecule, a complement thereof, a reverse complement thereof, or aportion thereof. In some aspects, the detection step comprisessequencing of (i) the nucleic acid molecule portion of the copy of thelabeled nucleic acid molecule, a complement thereof, a reversecomplement thereof, or a portion thereof, and (ii) the oligonucleotidetag portion of the copy of the labeled nucleic acid molecule, acomplement thereof, a reverse complement thereof, or a portion thereof.

In some aspects, the detection step may comprise sequencing the uniqueoligonucleotide tag-DNA junction, a complement of the uniqueoligonucleotide tag-DNA junction, a reverse complement of the uniqueoligonucleotide tag-DNA junction, or a portion thereof. In some aspects,the detection step may comprise sequencing the copy of the uniqueoligonucleotide tag-DNA junction, a complement of the copy of the uniqueoligonucleotide tag-DNA junction, a reverse complement of the copy ofthe unique oligonucleotide tag-DNA junction, or a portion thereof.

In another aspect, the labeled nucleic acid molecule is amplified. Inanother aspect, the copy of the labeled nucleic acid sequence isamplified. The amplification of the labeled nucleic acid molecule or thecopy of the labeled nucleic acid molecule may comprise a PCR-basedmethod. The PCR-based method may comprise qPCR. The PCR-based method maycomprise RT-PCR. The PCR-based method may comprise emulsion PCR. Theamplification of the nucleic acid molecule-labeled conjugate maycomprise a non-PCR-based method. The non-PCR-based method may comprisemultiple displacement amplification. The non-PCR-based method maycomprise random priming by a strand displacement polymerase.

In another aspect, the sample is from at least one single cell.Alternatively, the sample is from a plurality of cells. The sample maybe from less than about 100 cells.

In some aspects, the nucleic acid molecule is a DNA molecule. In anotheraspect, the nucleic acid molecule is an RNA molecule. The nucleic acidmolecule may be an mRNA molecule. The nucleic acid molecule may anoncoding RNA molecule. The noncoding RNA molecule may be a smallnoncoding RNA molecule. The noncoding RNA molecule may be a longnoncoding RNA molecule. The noncoding RNA molecule may be a microRNAmolecule. In some aspects, the oligonucleotide tag is attached to thenucleic acid molecule by ligation. In another aspect, theoligonucleotide tag is attached to the nucleic acid molecule byhybridization.

In another aspect is a method of counting or determining a number of DNAmolecules in a sample comprising: (a) providing a plurality ofoligonucleotide tags wherein a oligonucleotide tag comprises a uniqueidentifier sequence, a target sequence, and an optional PCR primersequence; (b) combining a sample comprising DNA molecules with theplurality of labeled primers to form a labeled DNA molecule, wherein thelabeled DNA molecule comprises a DNA molecule and a oligonucleotide tagand each target DNA molecule is capable of attaching to a differentoligonucleotide tag; and (c) detecting (i) the DNA molecule, acomplement of the DNA molecule, a reverse complement of the DNAmolecule, or a portion thereof, and (ii) the oligonucleotide tag, acomplement of the oligonucleotide tag, a reverse complement of theoligonucleotide tag, or a portion thereof to determine the count ornumber of different labeled DNA molecules, thereby counting ordetermining a number of DNA molecules in the sample.

In another aspect is a method of counting or determining a number of DNAmolecules in a sample comprising: (a) providing a plurality ofoligonucleotide tags wherein a oligonucleotide tag comprises a uniqueidentifier sequence, a target sequence, and an optional PCR primersequence; (b) combining a sample comprising DNA molecules with theplurality of labeled primers to form a labeled DNA molecule, wherein theattachment of the DNA molecule to the oligonucleotide tag forms a uniquemolecule-tag junction; and (c) detecting the unique molecule-tagjunction, a complement of the unique molecule-tag junction, a reversecomplement of the unique molecule-tag junction, or a portion thereof todetermine the count or number of different labeled DNA molecules,thereby counting or determining a number of DNA molecules in the sample.

In another aspect is a method for determining a copy number of a targetDNA in a sample comprising: (a) providing a plurality of adaptors,wherein the adaptors comprise a unique identifier sequence and eachadaptor is capable of attaching to a plurality of different DNAmolecules; (b) fragmenting a sample comprising genomic DNA to produce asample comprising DNA fragments; (c) combining a plurality of adaptorswith the sample comprising DNA fragments to form an adaptor-DNA fragmentconjugate, wherein substantially all of the DNA fragments are randomlyattached to an adaptor with a unique identifier sequence; and (d)detecting the adaptor, a complement of the adaptor, a reverse complementof the adaptor or a portion thereof to determine the number of differentadaptor-DNA fragment conjugates, thereby determining a copy number of atarget DNA.

In another aspect is a method determining a copy number of a target DNAmolecule in a sample comprising: (a) providing a plurality of adaptors,wherein the adaptors comprise a unique identifier sequence and theadaptors are capable of attaching to a plurality of different DNAmolecules; (b) fragmenting a sample comprising genomic DNA to produce asample comprising DNA fragments; (c) attaching adaptors to the DNAfragments, wherein substantially all of the DNA fragments capable ofbeing randomly attached to an adaptor with a unique identifier sequenceand the attachment of the adaptor to the DNA fragment forms a uniqueadaptor-DNA junction; and (d) detecting the unique adaptor-DNA junction,a complement of the unique adaptor-DNA junction, a reverse complement ofthe unique adaptor-DNA junction, or a portion thereof to determine thecount or number of different unique adaptor-DNA junctions, therebydetermining a copy number of a target DNA.

In some aspects, the adaptor comprises a ribonucleic acid. In someaspects, the ribonucleic acid is uracil. In some aspects, theribonucleic acid is cytosine. In some aspects, the ribonucleic acid isadenine. In some aspects, the ribonucleic acid is guanine.

In some aspects, the method further comprises synthesizing a copy of theadaptor-DNA fragment conjugate to replace a ribonucleic acid sequence inthe adaptor with a deoxyribonucleic acid sequence.

In some aspects, the detecting step comprises detecting the copy of theunique adaptor-DNA junction, a complement of the copy of the uniqueadaptor-DNA junction, a reverse complement of the copy of the uniqueadaptor-DNA junction, or a portion thereof. In some aspects, thedetecting step comprises detecting the copy of the adaptor, a complementof the copy of the adaptor, a reverse complement of the copy of theadaptor, or a portion thereof.

In some aspects, the detection step comprises hybridization of theunique adaptor-DNA junction, a complement of the unique adaptor-DNAjunction, a reverse complement of the unique adaptor-DNA junction, or aportion thereof to a solid support. In another aspect, the detectionstep comprises hybridization of the copy of the unique adaptor-DNAjunction, a complement of the copy of the unique adaptor-DNA junction, areverse complement of the copy of the unique adaptor-DNA junction, or aportion thereof to a solid support.

In some aspects, solid support comprises an array. In some aspects, thearray comprises probes attached to the surface. In some aspects, thearray comprises a probe feature for each unique-adaptor DNA junction. Insome aspects, the array comprises a probe feature for each copy of theunique-adaptor DNA junction. In another aspect, the solid supportcomprises a bead. In some aspects, the detection step comprisessequencing the unique adaptor-DNA junction, a complement of the uniqueadaptor-DNA junction, a reverse complement of the unique adaptor-DNAjunction, or a portion thereof. In some aspects, the detection stepcomprises sequencing the copy of the unique adaptor-DNA junction, acomplement of the copy of the unique adaptor-DNA junction, a reversecomplement of the copy of the unique adaptor-DNA junction, or a portionthereof.

In some aspects, the detection step comprises sequencing the copy of theadaptor, a complement of the copy of the adaptor, a reverse complementof the copy of the adaptor, or a portion thereof. In some aspects, theadaptor-DNA fragment conjugate is amplified.

In some aspects is a method of determining the presence or absence ofgenetic abnormalities comprising: (a) providing a plurality ofoligonucleotide tags wherein a oligonucleotide tag comprises a uniqueidentifier sequence, a target sequence, and an optional PCR primersequence; (b) combining a sample comprising genomic DNA with theplurality of labeled primers to form a genomic DNA-oligonucleotide tagconjugate, wherein each genomic DNA is capable of attaching to aoligonucleotide tag with a unique identifier sequence; and (c) detectingthe genomic DNA-oligonucleotide tag conjugate, a complement of genomicDNA-oligonucleotide tag conjugate, a reverse complement of the genomicDNA-oligonucleotide tag conjugate, or a portion thereof to count ordetermine a number of different genomic DNA-oligonucleotide tagconjugates, thereby determining the presence or absence of geneticabnormalities.

In some aspects, the detecting step comprises detecting the genomic DNA,a complement of the genomic DNA, a reverse complement of the genomicDNA, or a portion thereof. In some aspects, the detecting step comprisesdetecting the oligonucleotide tag, a complement of the oligonucleotidetag, a reverse complement of the oligonucleotide tag, or a portionthereof.

In some aspects, the genetic abnormality comprises an aneupoloidy. Theaneuploidy may be monosomy. The monosomy may be monosomy of the sexchromosome. The aneupoloidy may be trisomy. The trisomy may be trisomy21. The trisomy may be trisomy 18. The trisomy may be trisomy 13. Theaneuploidy may be tetrasomy. The aneuploidy may be pentasomy. In someaspects, the method further comprises diagnosing a genetic abnormality.In some aspects, the method may further comprise diagnosing Turnersyndrome. In some aspects, the method may further comprise diagnosingDown syndrome. In some aspects, the method may further comprisediagnosing Edwards syndrome. In some aspects, the method may furthercomprise diagnosing Patau syndrome. In some aspects, the geneticabnormality comprises a deletion in the genomic DNA. In some aspects,the genetic abnormality comprises a polymorphism. In some aspects, thegenetic abnormality comprises a single gene disorders. In some aspects,the genetic abnormality comprises a chromosome translocation.

In some aspects, the sample is from an embryo. In some aspects, thesample comprises at least one cell from the embryo.

In some aspects, the method further comprises determining animplantation status of the embryo based on the detecting step. In someaspects, the genomic DNA is fragmented prior to attachment of theoligonucleotide tags.

In some aspects, the genomic DNA is fragmented by a restriction enzyme.In some aspects, the genomic DNA is fragmented by an allele-specificrestriction enzyme.

In some aspects, the oligonucleotide tag comprises a ribonucleic acid.In some aspects, the ribonucleic acid is uracil. In some aspects, theribonucleic acid is cytosine. In some aspects, the ribonucleic acid isadenine. In some aspects, the ribonucleic acid is guanine. In someaspects, the method further comprises synthesizing a copy of the genomicDNA-oligonucleotide tag conjugate to replace a ribonucleic acid sequencein the oligonucleotide tag with a deoxyribonucleic acid sequence.

In some aspects, the detecting step comprises detecting the copy of thegenomic DNA-oligonucleotide tag conjugate, a complement of the copy ofthe genomic DNA-oligonucleotide tag conjugate, a reverse complement ofthe copy of the genomic DNA-oligonucleotide tag conjugate, or a portionthereof.

In some aspects, the copy of the genomic DNA-oligonucleotide tagconjugate is synthesized by a reverse transcriptase enzyme.

In some aspects, the detection step comprises hybridization of thegenomic DNA-oligonucleotide tag conjugate, a complement of the genomicDNA-oligonucleotide tag conjugate, a reverse complement of the genomicDNA-oligonucleotide tag conjugate, or a portion thereof to a solidsupport. In some aspects, the detection step comprises hybridization ofthe genomic DNA, a complement of the genomic DNA, a reverse complementof the genomic DNA, or a portion thereof to a solid support. In someaspects, the detection step comprises hybridization of theoligonucleotide tag, a complement of the oligonucleotide tag, a reversecomplement of the oligonucleotide tag, or a portion thereof to a solidsupport. In some aspects, the detection step comprises hybridization ofthe copy of the genomic DNA-oligonucleotide tag conjugate, a complementof the copy of the genomic DNA-oligonucleotide tag conjugate, a reversecomplement of the copy of the genomic DNA-oligonucleotide tag conjugate,or a portion thereof to a solid support. In some aspects, the detectionstep comprises hybridization of the copy of the genomic DNA, acomplement of the copy of the genomic DNA, a reverse complement of thecopy of the genomic DNA, or a portion thereof to a solid support. Insome aspects, the detection step comprises hybridization of the copy ofthe oligonucleotide tag, a complement of the copy of the oligonucleotidetag, a reverse complement of the copy of the oligonucleotide tag, or aportion thereof to a solid support.

In some aspects, the detection step comprises sequencing of the genomicDNA-oligonucleotide tag conjugate, a complement of the genomicDNA-oligonucleotide tag conjugate, a reverse complement of the genomicDNA-oligonucleotide tag conjugate, or a portion thereof. In someaspects, the detection step comprises sequencing of the genomic DNA, acomplement of the genomic DNA, a reverse complement of the genomic DNA,or a portion thereof. In some aspects, the detection step comprisessequencing of the oligonucleotide tag, a complement of theoligonucleotide tag, a reverse complement of the oligonucleotide tag, ora portion thereof. In some aspects, the detection step comprisessequencing of the copy of the genomic DNA-oligonucleotide tag conjugate,a complement of the copy of the genomic DNA-oligonucleotide tagconjugate, a reverse complement of the copy of the genomicDNA-oligonucleotide tag conjugate, or a portion thereof. In someaspects, the detection step comprises sequencing of the copy of thegenomic DNA, a complement of the copy of the genomic DNA, a reversecomplement of the copy of the genomic DNA, or a portion thereof. In someaspects, the detection step comprises sequencing of the copy of theoligonucleotide tag, a complement of the copy of the oligonucleotidetag, a reverse complement of the copy of the oligonucleotide tag, or aportion thereof.

In some aspects, the genomic DNA-oligonucleotide tag conjugate isamplified. In some aspects, the copy of the genomic DNA-oligonucleotidetag conjugate is amplified.

Further disclosed herein are kits and compositions for stochasticallylabeling a molecule (e.g., nucleic acids such as DNA and RNA molecules,or polypeptides such as proteins and enzymes). In some instances, thekits and compositions are used for stochastically labeling apolyadenylated molecule. The polyadenylated molecule can be apolyadenylated RNA molecule. Alternatively, the kits and compositionsare used for stochastically labeling a DNA molecule.

In some instances, the kits comprise a stochastic label primer,universal PCR primer, dye-labeled primer, reverse transcriptase, UDGenzyme, polymerase, buffers, dNTP, array, gene specific primers, targetspecific primers, control oligo, or any combination thereof.Alternatively, the kits comprise a) a universal PCR primer; b) a Cy3labeled universal PCR primer; c) a Cy3 TrueTag Grid; and d) an array.The array can be a 2×8 array. The kits disclosed herein can furthercomprise a stochastic label primer, carrier, control oligo, reversetranscriptase, UDG enzyme, polymerase, gene specific primers, targetspecific primers, dNTP, or any combination thereof.

The stochastic label primer can comprise a primer attached to anoligonucleotide tag, wherein the oligonucleotide tag comprises an oligodT sequence, a unique identifier region, and a universal primer bindingsite, and wherein the universal primer binding site can enable annealingof the universal PCR primer of the kit to the stochastic label primer.In some instances, a stochastic label oligo dT primer is anoligonucleotide tag attached to an oligo dT primer.

The dye-labeled primer can comprise a primer labeled with a dye. Theprimer can be a universal PCR primer. Alternatively, the primer is atarget-specific primer. The dye can be a fluorescent dye. In someinstances, the dye is a Cy™ dye. In some instances, the Cy™ dye is a Cy3dye.

The kits and compositions disclosed herein can further comprise aplurality of probes. In some instances, the plurality of probes ishybridized to the array. The plurality of probes can allow hybridizationof the labeled-molecule to the array. The plurality of probes cancomprise a sequence that is complementary to the stochastic label oligodT. Alternatively, or additionally, the plurality of probes comprises asequence that is complementary to the molecule.

The kits and compositions disclosed herein can further comprise one ormore reagents to remove non-labeled molecules, excess primers, or excessoligonucleotide tags (or stochastic label primers) from the samplecomprising labeled-molecules.

In some instances, the kits and compositions comprise a reversetranscriptase enzyme. The reverse transcriptase can be MMLV reversetranscriptase.

The kits and compositions can comprise a polymerase enzyme. Thepolymerase can be a Taq polymerase. For example, the Taq polymerase is aTitatium Taq polymerase.

In some instances, the kits and compositions comprise an enzyme. Theenzyme can be an RNase enzyme. Alternatively, the enzyme is UDG. Inother instances, the enzyme is a restriction enzyme. The enzyme can be aprotease. In some instances, the enzyme is a DNase enzyme.Alternatively, the enzyme is a ligase. The kits and compositions cancomprise one or more reagents that can deactivate an enzyme disclosedherein.

In some instances, the kit further comprises a carrier substance. Thecarrier substance can increase the efficiency of a reaction (e.g.,amplification, reverse transcription, ligation, hybridization). Thecarrier substance can be a nucleic acid molecule. The nucleic acidmolecule can be an RNA molecule. The RNA molecule can be apolyadenylated RNA or phage RNA. The phage RNA can be RNA from a MS2phage. Alternatively, the nucleic acid molecule is a plasmid.

The kit can further comprise a solid support. The solid support can be abead. The bead can hybridize to the labeled-molecule. The bead canenable detection of the labeled molecule. The bead can be a streptavidinbead or biotin-labeled bead.

The kit can further comprise an algorithm for detecting and/orquantifying the labeled-molecule. Alternatively, or additionally, thekit comprises a software program for detecting/and or quantifying thelabeled-molecule. In some instances, the kits further comprise a thermalcycler. The kits can further comprise one or more components forsequencing the labeled-molecule. The one or more components forsequencing can comprise a sequencer, one or more primers for sequencing,beads for sequencing, or any combination thereof. The kit can furthercomprise one or more components for detecting and/or quantifying thelabeled-molecule. The one or more components for detecting and/orquantifying the labeled-molecule can comprise an array detector, arrayreader, bead detector, scanner, fluorometer, or any of the instrumentsor components disclosed herein.

EXAMPLES Example 1 Absolute Counting Protocol

Part 1. Reverse Transcription and Stochastic Labeling

In this step, the stochastic labels are annealed to the poly A RNA. Toincrease the overall efficiency of the subsequent reverse transcriptionreaction, a large amount of carrier RNA is also added to the sample.

In some instances, tips with low nucleic acid binding properties areused when pipetting extremely low concentrations of RNA. These specialtips can be used for pipetting the RNA sample into the annealing mastermix. If a dilution of the RNA is needed, low binding tubes can be usedas well. Once the RNA has been added to the annealing master mix,regular tubes/tips can be used.

Make a master mix by combining the reagents listed below:

Water 7.8 μl K562 Total RNA (1 μg/μl) 1 μl 10 mM dNTP 1 μl Gene SpecificdUTP Primer (10 μM) 0.4 μl Stochastic Labels (10 μM)* 0.4 μl Total 10.6μl

Add 2 μl of the RNA sample to be analyzed.

Mix well by pipetting and spin briefly

Incubate at 65° for 5 minutes (Program 1), and then place the tubes onice for at least 1 minute.

In this step, double stranded cDNA is created for the specific gene ofinterest. Each cDNA molecule will now contain a primer site for thesubsequent PCR step. Combine the following to make a master mix forreverse transcription:

5X First Strand Buffer 4 μl 0.1M DTT 1 μl SuperRNaseIn (20 U/μl) 1 μlMMLV RT 1 μl NEB Taq Polymerase 0.4 μlThe use MMLV RT and NEB Taq Polymerase instead of Superscript III andTitanium Taq can alternatively be used

Add 7.4 μl of master mix to each tube and mix by pipetting gently. Spinbriefly.

Run the following program (Program 2) on the thermal cycler:

37° for 60 minutes3 cycles of:94° for 2 minutes55° for 2 minutes68° for 2 minutesThen 4° forever

After the PCR reaction, it is necessary to digest the sample with UracilDNA Glycosylase (UDG) to prevent the unincorporated primer from beingamplified in the gene specific PCR.

To each reaction, add 0.5 μl of UDG. Mix very well by pipetting.Transfer all liquid to a new PCR tube to ensure that there is nocarryover of unmixed sample.

Incubate at 37° for 30 minutes, then 4°.

Part 2. Initial Gene Specific PCR

Combine the following reagents to make a master mix for PCR:

Nuclease-free water 10.9 μl 10X NEB Taq Buffer 1.5 μl 10 mM dNTP 0.3 μlGene Specific Primer (1 μM) 1 μl Universal PCR primer (1 μM)* 1 μl NEBTaq Polymerase 0.3 μl Total 15 μl

Final concentration of 0.05 uM primer increases specificity of products

Add 5 μl of labeled product from the previous step to a new PCR tube.Add 15 μl PCR master mix to each sample.

Mix well by pipetting and spin briefly.

Run the following program (Program 4) on the thermal cycler:

94° for 2 minutes30 cycles of:94° for 2 minutes55° for 2 minutes68° for 2 minutesThen 68° for 4 minutes4° forever

Part 3. Second, Nested PCR

Prepare the master mix for the second, nested, PCR in the pre-PCR area.

Nuclease-free water 39.5 μl 10X NEB Taq Buffer 5 μl 10 mM dNTP 1 μl GeneSpecific Nested Primer (10 μM) 1 μl 5Tye563 Labeled Universal PCR primer(10 μM)* 1 μl NEB Taq Polymerase 0.5 μl Total 48 μl

Aliquot 48 μl of master mix to a new PCR tube.

Add 2 μl from the first PCR reaction to the tube in a separate roomdesignated for post amplification processing to avoid contamination ofthe pre-PCR area. Perform all subsequent steps in this area.

Mix well by pipetting and spin briefly.

Run the following program (Program 4) on the thermal cycler:

94° for 2 minutes30 cycles of:94° for 2 minutes55° for 2 minutes68° for 2 minutesThen 68° for 4 minutes4° forever

Optional Step: Run 4 ul of PCR product on a polyacrylamide 4-20%gradient TBE gel to assess size and purity

Part 4. Target Hybridization

Turn hyb oven on at 37°.

Prepare samples for hybridization to an Applied Microarray Inc. arrayslide. Add the following in a 0.2 mL PCR tube:

Wash A (6X SSPE + 0.01% Triton X-100) 55 μl Cy3 Control Oligo (760 pM)*1 μl PCR product 20 μl Total 76 μl

Mix by pipetting and spin briefly.

Incubate tubes at 95° to denature and then place on ice.

Remove adhesive seal from AMI array slide. Pipet each hybridizationcocktail into a well of the AMI array slide. Make a note of the order inwhich the targets are added. Cover slide with second strip of adhesive(included)

Place sealed array slide into humidity chamber and put intohybridization oven. Incubate at 37° overnight.

Part 5. Array Wash and Scan

After the overnight hybridization, take the array slide out of thehybridization oven and remove adhesive cover. Pipet out remaininghybridization cocktail and save at −20° if desired.

Dispense 150 μl Wash A to each used well. Aspirate liquid and dispense150 μl Wash B (0.6×SSPE+0.01% Triton X-100) to each well. Aspirateliquid and bring array slide to scanner as the arrays will be scanneddry.

Turn on the Sensovation FLAIR instrument. Wait 10 minutes for themachine to warm up.

Open the software and click, “Tray Open”. Place the array slide into the4-slide holder. Be sure to seat the slide properly. In the software,click “Tray Close”.

Click the “Scan” Icon. A window appears with information about the scanto be performed. Modify the name of the scan if desired and select theappropriate wells to be scanned by clicking the “ . . . ” icon in the“scan positions” field. Click each well that is to be scanned. Thesoftware will circle each selected well in yellow. Click “ok”.

The Plate Overview window will appear showing the progress of the scan.Once a well is scanned, the color on the screen will turn from grey togreen if the reference pattern has been detected and the grid has beenpositioned. If the reference pattern has not been detected, the wellwill be colored red. If any of the scans do not detect the reference,the grid may be manually aligned by clicking the “reanalyze” button atthe top of the screen. This will display the grid, which can bepositioned properly. Click the green “accept analysis” button at the topof the screen.

Once all of the grids have been aligned, the data can be exported. Toobtain windows functionality, press the “windows” key on the keyboardand “D” simultaneously. Locate the scan results in the “my documents”folder under ArrayReader/sensovation/arrayreader.scanresults. Open theappropriate scan folder and copy the TIFF images and the result .csvfiles to a flash drive or transfer through the network.

Proceed to data analysis either manually or with a computer softwarepackage.

Example 2 Four Experiments where 120 RNA Molecules were Added to aSample of Background Total RNA

240 copies of a polyadenylated nucleic acid fragment was added to a 10μL reaction containing 1× titanium Taq DNA polymerase buffer, 0.2 μMdNTPs, 0.2 μM of a pool of 960 oligo (dT) stochastic labels, 0.2 μM of asecond strand cDNA primer and 0.2 μL of Taq DNA polymerase. In somereactions, an additional number of polyadenylated DNA fragments withsequences unrelated to the 240 copies of test nucleic acid fragment werealso added. In reaction A, 1×10¹⁰ background polyadenylated DNAmolecules were added to the reaction. In reaction B, 1×10⁹ backgroundpolyadenylated DNA molecules were added to the reaction. In reaction C,1×10⁶ background polyadenylated DNA molecules were added to thereaction. And, in reaction D, no background polyadenylated DNA moleculeswere added to the reaction. 10 ng, 1 ng or 1 pg of randomly fragmentedand polyadenylated human genomic DNA was tested. After 3 cycles ofincubation at 94° C. for 2 min, 45° C. for 2 min and 65° C. for 5 min, 1unit of Uracil DNA glycosylase is added and the reaction is incubatedfor 30 min at 37° C. Half of the reaction is then added into a 20 μL PCRreaction consisting of 1× Titanium buffer, 0.2 μM dNTP, 0.2 μMgene-specific forward primer, 0.2 μM universal reverse primer and 0.3 μLTitanium Taq polymerase. PCR conditions were 94° C. for 2 min followedby 30 cycles of 94° C. for 20 sec, 58° C. for 20 sec and 68° C. for 20sec. A final incubation at 68° C. for 4 min was performed. A nested PCRis performed following the same conditions as the first PCR, except thata nested Forward primer was used. 2 μL of a 1:25 dilution of the initialPCR was used as template for the nested PCR. PCR products were randomlyfragmented with DNase, biotin-labeled with Terminal transferase enzymeand then hybridized to a detector array for 12 hours at 37° C. Signalsfrom hybridized DNAs were detected via staining with Streptavidinconjugated Phycoerytherin and imaging on a microarray scanner. FIG. 2A-Dshows the signals from hybridized DNAs for reactions A-D, respectively.The number of labels present in the hybridized DNA is counted and usedto determine the number of original copies of nucleic acid fragments.

Reaction # of labels # of original copies A 122 130 B 116 124 C 109 114D 115 122

Example 3 Comparison with Digital PCR

The concentration of an in vitro transcribed RNA was determined using anAgilent bioanalyzer instrument. 0.5 μg of the RNA was mixed with 2 μg ofa K562 cell line total RNA which was used as a carrier. The RNA mixturein 3 μL was added to 1 μL of a 10 mM dNTP solution and 2 μL of a 10 μMpool of 960 oligo (dT) labels and 7 μL of water. This mixture wasincubated at 65° C. for 5 min and immediately chilled on ice. 4 μL of afirst strand reaction buffer (250 mM Tris-HCl (pH 8.3 at 25° C.), 375 mMKCl), 1 μL of 0.1 M DTT, 1 μL of RNase inhibitor (20 units) and 1 μL ofsuperscript II reverse transcriptase (200 units) was added and thereaction was incubated at 50° C. for 60 min and then at 70° C. for 15min. 1 μL of RNase H (2 units) was added and the reaction was incubatedat 37° C. for 20 min. Digital PCR was used to quantitate the number ofcopies of cDNA synthesized from the in vitro transcribed RNA. The samplewas also test by stochastic labeling PCR. 90 copies of the cDNA (asdetermined by digital PCR) was added to a 10 μL reaction containing 1×titanium PCR buffer, 0.2 μM dNTPs and 0.2 μL of titanium taq polymerase.The reaction was incubated for 3 cycles at 94° C. for 2 min, 55° C. for2 min and 68° C. for 2 min. 1 unit of uracil DNA glycosylase was addedand the reaction was incubated at 37° C. for 30 min. First and nestedPCRs, fragmentation, biotin-labeling and array detection were performedas described in Example 2. FIG. 3 shows the signals from the labels inthe hybridized DNA. The number of labels present in the hybridized DNAis counted and used to determine the number of original copies ofnucleic acid fragments. 40 labels were present in the hybridized DNA and41 copies were determined by stochastic labeling, as compared to 43copies as determined by digital PCR. These results demonstrate thatstochastic labeling is an effective method for determining the count ofa molecule and its accuracy is comparable to digital PCR.

Example 4 RT Yield Increased with Reaction Carriers

To test the effectiveness of carrier RNAs on improving the reversetranscription yield and as a means to reduce non-specific RNA or cDNAlosses during reactions, copies of an in vitro transcribedpolyadenylated RNA was tested with stochastic labeling following theprotocol described in example 2. Additionally, total RNA isolated frommammalian cells, yeast, or E. coli, short polyadenylated syntheticribonucleotide, yeast tRNA, or MS2 phage RNA were added to the reactionmixture. Each reaction used anywhere between 0.5 μg to 2 μg of carrierRNA. The number of RNA molecules reverse transcribed to cDNA wasdetermined by the number of observed labels detected on the array, andin each case, the effectiveness of each carrier RNA tested could beeasily determined. FIG. 4A-D shows the observed labels for reactionsA-D, respectively.

# of Reaction # of Input molecules Carrier RNA RNase H labels A 188Total RNA from X — 158 B 188 MS2 phage RNA — 165 C 188 Yeast tRNA — 1 D188 — RNase H 154

Example 5 Comparison of MMLV and RNase H Minus MMLVreverse Transcriptase

The performance of the wild type MMLV reverse transcriptase was comparedwith the RNase H minus mutant version (Superscript III) of the enzyme.375 copies of an in vitro transcribed polyadenylated RNA was added to acarrier of 1 μg of a K562 cell line total RNA. The RNAs were added intoa 12.6 μL reaction containing 1 μL of a 10 mM dNTP solution, 0.4 μL of a10 μM second strand primer, 0.4 μL of a 10 μM pool of 960 oligo(dT)labels. The reaction was incubated at 65° C. for 5 min to denature theRNA, and then quickly chilled on ice. 4 μL of a 5× first strand buffer,1 μL of a 0.1M DTT, 1 μL of superase RNase inhibitor (20 units) and 0.4μL of Taq DNA polymerase (2 units) was added. Additionally, in reactionA, 1 μL (200 units) of the RNase H minus mutant (Superscript III) wasadded. And, in reaction B, 1 μL (200 units) of the wild type MMLVreverse transcriptase was added. The reactions were incubated at 42° C.for 60 min, followed by 3 cycles of 94° C. for 2 min, 55° C. for 2 minand 68° C. for 2 min. 1 unit of uracil DNA glycosylase was added and thereaction was mixed and moved to a new tube and incubated at 37° C. for30 min. 5 μL of the reaction was then added to a 20 μL PCR reactionconsisting of 1× Titanium buffer, 0.2 μM dNTP, 0.2 uM gene-specificforward primer, 0.2 μM universal reverse primer and 0.3 μL Titanium Taqpolymerase. PCR conditions were 94° C. for 2 min followed by 30 cyclesof 94° C. for 20 sec, 58° C. for 20 sec and 68° C. for 20 sec. A finalincubation at 68° C. for 4 min was performed. A nested PCR is performedfollowing the same conditions as the first PCR, except that a nestedForward primer was used. 2 μL of a 1:25 dilution of the initial PCR wasused as template for the nested PCR. PCR products were randomlyfragmented with DNase, biotin-labeled with Terminal transferase enzymeand then hybridized to a detector array for 12 hours at 37° C. Signalsfrom hybridized DNAs were detected via staining with Streptavidinconjugated Phycoerytherin and imaging on a microarray scanner. FIG. 5A-Bshow the labels present in the hybridized DNA in reactions A and B,respectively. The number of labels present in the hybridized DNA iscounted and used to determine the number of original copies of nucleicacid fragments.

# Input RNA Reaction molecules Reverse Transcriptase # of labels A 188Superscript III 159 B 188 MMLV 124

Example 6 Comparison of Polymerases for Second Strand Synthesis

The performance of Taq polymerase was compared to Titanium Taqpolymerase. 1875 copies of an in vitro transcribed polyadenylated RNAwas added to reaction A. 188 copies of an in vitro transcribedpolyadenylated RNA was added to reaction B. 1875 copies of an in vitrotranscribed polyadenylated RNA was added to reaction C. And, 188 copiesof an in vitro transcribed polyadenylated RNA was added to reaction D. 1μg of carrier RNA from a K562 cell line was added to each of thereaction mixtures. The RNAs were added into a 12.6 μL reactioncontaining 1 μL of a 10 mM dNTP solution, 0.4 μL of a 10 μM secondstrand primer, 0.4 μL of a 10 μM pool of 960 oligo(dT) labels. Thereactions were incubated at 65° C. for 5 min to denature the RNA, andthen quickly chilled on ice. 4 μL of a 5× first strand buffer, 1 μL of a0.1M DTT, 1 μL of superase RNase inhibitor (20 units), reversetranscriptase, and 0.4 μL of Taq DNA polymerase (2 units) were added toeach reaction. The reactions were incubated at 42° C. for 60 min,followed by 3 cycles of 94° C. for 2 min, 55° C. for 2 min and 68° C.for 2 min. 1 unit of uracil DNA glycosylase was added and the reactionwas mixed and moved to a new tube and incubated at 37° C. for 30 min. 5μL of reactions A and B were mixed with a 20 μL PCR reaction consistingof 1× Taq buffer, 0.2 μM dNTP, 0.2 uM gene-specific forward primer, 0.2μM universal reverse primer and 0.3 μL Taq polymerase. 5 μL of reactionsC and D were mixed with a 20 μL PCR reaction consisting of 1× Titaniumbuffer, 0.2 μM dNTP, 0.2 uM gene-specific forward primer, 0.2 μMuniversal reverse primer and 0.3 μL Titanium Taq polymerase. PCRconditions were 94° C. for 2 min followed by 30 cycles of 94° C. for 20sec, 58° C. for 20 sec and 68° C. for 20 sec. A final incubation at 68°C. for 4 min was performed. A nested PCR is performed following the sameconditions as the first PCR, except that a nested Forward primer wasused. 2 μL of a 1:25 dilution of the initial PCR was used as templatefor the nested PCR. PCR products were randomly fragmented with DNase,biotin-labeled with Terminal transferase enzyme and then hybridized to adetector array for 12 hours at 37° C. Signals from hybridized DNAs weredetected via staining with Streptavidin conjugated Phycoerytherin andimaging on a microarray scanner. FIG. 6A-D shows the labels present inthe hybridized DNA in reactions A-D, respectively. The number of labelspresent in the hybridized DNA is counted and used to determine thenumber of original copies of nucleic acid fragments.

# Input RNA Reaction molecules Polymerase # of labels A 1875 Taq — B 188Taq 157 C 1875 Titanium Taq — D 188 Titanium Taq 129

Example 7 Absolute Quantitation of mRNA by Counting Individual DNAMolecules

mRNA molecules can be quantitated by the addition of labels prior toamplification of cDNA molecules (FIG. 19). Labeled cDNA molecules areformed by cDNA synthesis of an mRNA molecule by the addition of adeoxy-oligonucleotide primer with (1) an oligo dT sequence to anneal tothe poly-A RNA tail; (2) a collection of predetermined or randomsequence label tags; and (3) a common or universal PCR primer sequence.The labeled cDNA molecules are amplified using gene-specific primers anda common or universal PCR primer. After amplification, the number oflabels of different sequence composition can be readily detected byhybridization, sequencing or other detection methods. The difficult taskof counting the number of individual mRNA molecules in solution istransformed into the simple task of determining the number of types ofdifferent labels, each being present at high concentrations followingamplification, provided that the initial label sequence diversity issufficiently greater than the number of molecules present. Any othersuitable method can also be used to incorporate labels into the RNA orcDNA molecules before or during amplification. Any other PCR or non-PCRbased methods can also be used to amplify the RNA or cDNA molecules.Although helpful in these examples, amplification of the labeledmolecules may not be required for detection.

Example 8 Digital Microarray for RNA Expression

The mRNA is reverse transcribed using a pool of n oligo-dT label primers(random primers with labels may also be used) (FIG. 20). The cDNA can beoptionally amplified with methods such as PCR and T7 amplification. Thelabels are amplified along with each cDNA molecule. cDNAs are hybridizedto digital arrays to determine the number of distinct labels for eachgene of interest. Hybridization requires both presence of the genesequence, most likely a segment on the 3′ exon of the gene, and one ofthe label sequences. An array with 7 million features is sufficient todetect a collection of 350 labels applied to a sample with 20,000different mRNA sequences to determine the number of copies of each mRNApresent in the sample. A subset of the 350 label primers may be appliedat a lower concentration to increase the effective dynamic range ofmeasurement. This method is particularly advantageous for samplinglimiting amounts of starting material, such as in single cells.

Example 9 Digital Microarray for DNA Copy Number

Genomic DNA is digested into small fragments in one or more reactionsusing one or more restriction enzymes. Adaptors with label sequences areligated to the DNA fragments (FIG. 21). The ligated fragments areoptionally amplified. Ligated fragments may optionally be digested withone or more restriction enzymes prior to amplification to prevent thereplication of certain fragments, which is useful in the selectiveamplification of only fragments of interest. Hybridization to digitalarrays detects the number of distinct labels ligated to each restrictedfragment. Using 350 label sequences, an array of 7 million features canassay 20,000 fragments in the genome, which represents average intervalsof 150 kb in humans. Additionally, some allele specific fragments may beassayed by choosing restriction enzymes (e.g., 4 base cutters) specificfor an allele of interest.

Example 10 Digital Microarray for microRNAs

Labels are attached to the 3′ and 5′ ends of microRNA by ligation orother means (FIG. 22). The label-microRNA complex is reverse transcribedto generate label-DNA products. The label-DNA products are optionallyamplified. The label-DNA products are hybridized on digital array todetect the number of labels per microRNA. miRBase 18(http://www.mirbase.org/) was released in November 2011 and lists 1921unique mature human miRNAs. An array of 2 million features canadequately detect 1000 labels ligated to the 1921 miRNAs.

Example 11 Digital Microarray for Single Cell Pre-Implantation GeneticDiagnosis (PGD)

Primary challenge with single-cell genomic DNA amplification assays isfrom allele dropout and replication bias. As shown in the computationmodeling analysis in FIG. 43 where every molecule has a 0.8 probabilityof replication, molecules of 1:1 initial copy ratios can easily bedistorted to 1:10 or greater just after a few replication cycles.

However, when labels are first attached prior to amplification, countinglabels to determine copy number is unaffected by replication bias, solong as replication occurs. Although, this does not solve the problem ofallele dropouts, aneuploidy determination and large regions of deletionor amplification can be easily and accurately determined. This isparticularly useful for PGD applications.

Example 12 Digital Microarray for Measuring Fetal Aneuploidy in MaternalCirculating Nucleic Acids

Digital microarray can be used to measure fetal aneuploidy in maternalcirculating nucleic acids. A sample comprising maternal circulatingnucleic acids is provided. The DNA is fragmented using a 4 base cutter.Labels are attached to the fragmented DNA. Circulate and multiplex PCRto amplify 40 chromosome 21 markers and 10 control chromosome markers.Detect amplified label-DNA products on an array of 5 million features.The number of copies of chromosome 21 can be used to determine theoccurrence of fetal aneuploidy (FIG. 24).

Example 13 Absolute Quantitation of mRNA by Counting Individual DNAMolecules

mRNA molecules can be quantitated by the incorporation of labels duringfirst-strand cDNA synthesis (FIG. 25). Labeled cDNA molecules are formedby cDNA synthesis of an mRNA molecule by the addition of adeoxy-oligonucleotide primer with (1) an oligo dT sequence to anneal tothe poly-A RNA tail; (2) a collection of predetermined or randomsequence label tags; and (3) a common or universal PCR primer sequence.After first-strand cDNA synthesis, the number of labels of differentsequence composition can be readily detected by hybridization,sequencing or other detection methods. The difficult task of countingthe number of individual mRNA molecules in solution is transformed intothe simple task of determining the number of types of different labels,each being present at high concentrations following amplification,provided that the initial label sequence diversity is sufficientlygreater than the number of molecules present. Any other suitable methodcan also be used to incorporate labels into the RNA or cDNA moleculesbefore or during first-strand cDNA synthesis.

Example 14 Titration Experiment with Serial Dilutions of Kanamycin RNA

A titration curve was generated by performing serial dilutions ofkanamycin RNA to illustrate the broad dynamic range of the absolutecounting protocol. Each of 9 serial dilutions was normalized to aconcentration of 0.25 fg/μl from 2.5 pg/μl, 1.25 pg/μl, 0.25 pg/μl,0.125 pg/μl, 0.025 pg/μl, 12.5 fg/μl, 2.5 fg/μl, 1.25 fg/μl and 0.25fg/μl. All of the dilutions were made using a dilution solution of 1ng/μl E. Coli total RNA in tubes pre-rinsed with a solution of 10 ng/μlyeast RNA to hinder the sticking of the sample RNA to the walls of thetube. The samples were added to a 12.6 μl reaction containing 1 μg E.Coli total RNA, 1 μl of a 10 mM solution of dNTP's, 0.4 μl of a 10 uM dUprimer specific for kanamycin and 0.4 μl of a 10 μM pool of 960 dT oligolabels. The reaction was incubated at 65° C. for 5 min to denature theRNA, and then quickly chilled on ice. 4 μL of a 5× first strand buffer,1 μL of a 0.1M DTT, 1 μL of superase RNase inhibitor (20 units), 1 μL(200 units) of the wild type MMLV reverse transcriptase and 0.4 μL ofTaq DNA polymerase (2 units) were added. The reactions were incubated at37° C. for 60 min, followed by 3 cycles of 94° C. for 2 min, 55° C. for2 min and 72° C. for 2 min. 1 unit of uracil DNA glycosylase was addedand the reaction was mixed and moved to a new tube and incubated at 37°C. for 30 min. 5 μL of the reaction was then added to a 20 μL PCRreaction consisting of 1× Taq Reaction buffer, 0.2 μM dNTP, 0.05 uMgene-specific forward primer, 0.05 μM universal reverse primer and 0.3μL Taq polymerase. PCR conditions were 94° C. for 2 min followed by 30cycles of 94° C. for 20 sec, 58° C. for 20 sec and 72° C. for 20 sec. Afinal incubation at 72° C. for 4 min was performed. A nested PCR wasperformed using a nested forward primer and the universal reverse primerwith a Cy3 label attached. 0.5 μl of the initial PCR was used astemplate for the nested PCR. PCR conditions were the same as for thefirst PCR except that the 58° C. step was performed at 55° C. Thesamples were hybridized to a detector array at 37° C. overnight andscanned the following day using a fluorescence reader to detect whichpositions on the array contained the Cy3 label. The number of positivespots was used to determine the initial concentration of sample. FIG. 35shows the dilution scheme. FIG. 36A-H shows the scatter plots of resultsand Table 1 shows the results. FIG. 37 shows the correlation graph.

TABLE 1 Dilution Expected Actual FIG Initial Concentration Factor CountCount 36A 2.5 pg/μL 10000 130 199 36B 1.25 pg/μL 5000 130 178 36C 0.25pg/μL 1000 130 170 36D 0.125 pg/μL 500 130 153 36E 1.025 pg/μL 50 130154 36F 12.5 fg/μL 10 130 117 36G 2.5 fg/μL 5 130 95 36H 1.25 fg/μL 1130 137

Example 15 Titration Experiment with Serial Dilutions of Human Liver RNAto Measure GAPDH Expression

A titration curve was generated by performing serial dilutions of humanliver total RNA to illustrate the ability of the stochastic labelingprotocol to detect levels of gene expression. Each of 8 serial dilutionswas normalized to a concentration of 1.25 pg/μl from 5000 pg/μl, 1250pg/μl, 500 pg/μl, 125 pg/μl, 50 pg/μl, 12.5 pg/μl, 5 pg/μl and 1.25pg/μl. All of the dilutions were made using a dilution solution of 1ng/μl E. Coli total RNA in tubes pre-rinsed with a solution of 10 ng/μlyeast RNA to hinder the sticking of the sample RNA to the walls of thetube. The samples were added to a 12.6 μl reaction containing 1 μg E.Coli total RNA, 1 μl of a 10 mM solution of dNTP's, 0.4 μl of a 10 uM dUprimer specific for GAPDH and 0.4 μl of a 10 μM pool of 960 dT oligolabels. The reaction was incubated at 65° C. for 5 min to denature theRNA, and then quickly chilled on ice. 4 μL of a 5× first strand buffer,1 μL of a 0.1 M DTT, 1 μL of superase RNase inhibitor (20 units), 1 μL(200 units) of the wild type MMLV reverse transcriptase and 0.4 μL ofTaq DNA polymerase (2 units) was added. The reactions were incubated at37° C. for 60 min, followed by 3 cycles of 94° C. for 2 min, 55° C. for2 min and 72° C. for 2 min. 1 unit of uracil DNA glycosylase was addedand the reaction was mixed and moved to a new tube and incubated at 37°C. for 30 min. 5 μL of the reaction was then added to a 20 μL PCRreaction consisting of 1× Taq Reaction buffer, 0.2 μM dNTP, 0.05 uMgene-specific forward primer, 0.05 μM universal reverse primer and 0.3μL Taq polymerase. PCR conditions were 94° C. for 2 min followed by 30cycles of 94° C. for 20 sec, 58° C. for 20 sec and 72° C. for 20 sec. Afinal incubation at 72° C. for 4 min was performed. A nested PCR wasperformed using a nested forward primer and the universal reverse primerwith a Cy3 label attached. 0.5 μl of the initial PCR was used astemplate for the nested PCR. PCR conditions were the same as for thefirst PCR except that the 58° C. step was performed at 55° C. Thesamples were hybridized to a detector array at 37° C. overnight andscanned the following day using a fluorescence reader to detect whichpositions on the array contained the Cy3 label. The number of positivespots was used to determine the initial concentration of sample. FIG. 38shows the dilution scheme. FIG. 39 shows the scatter plots of resultsand Table 2 shows the results. FIG. 40 shows and correlation graph.

TABLE 2 FIG Initial Concentration Dilution Factor Actual Count 39A 5000pg/μL 4000 73 39B 1250 pg/μL 1000 63 39C 500 pg/μL 400 69 39D 125 pg/μL100 46 39E 50 pg/μL 40 65 39F 12.5 pg/μL 10 38 39G 5 pg/μL 4 53 39H 1.25pg/μL 1 37

Example 16 Measurements of Control Bacterial Genes

The protocol was validated using Poly A bacterial control RNAs (Lys,Thr, Dap and Phe), as well as RNA from the Kanamycin resistance gene. 4different dilutions of each control were used to validate the accuracyof the counts. The samples were added to a 12.6 μl reaction containing 1μg E. Coli total RNA, 1 μl of a 10 mM solution of dNTP's, 0.4 μl of a 10uM gene specific dU primer and 0.4 μl of a 10 μM pool of 960 dT oligolabels. The reaction was incubated at 65° C. for 5 min to denature theRNA, and then quickly chilled on ice. 4 μL of a 5× first strand buffer,1 μL of a 0.1 M DTT, 1 μL of superase RNase inhibitor (20 units), 1 μL(200 units) of the wild type MMLV reverse transcriptase and 0.4 μL ofTaq DNA polymerase (2 units) was added. The reactions were incubated at37° C. for 60 min, followed by 3 cycles of 94° C. for 2 min, 55° C. for2 min and 72° C. for 2 min. 1 unit of uracil DNA glycosylase was addedand the reaction was mixed and moved to a new tube and incubated at 37°C. for 30 min. 5 μL of the reaction was then added to a 20 μL PCRreaction consisting of 1× Taq Reaction buffer, 0.2 μM dNTP, 0.05 uMgene-specific forward primer, 0.05 μM universal reverse primer and 0.3μL Taq polymerase. PCR conditions were 94° C. for 2 min followed by 30cycles of 94° C. for 20 sec, 58° C. for 20 sec and 72° C. for 20 sec. Afinal incubation at 72° C. for 4 min was performed. A nested PCR wasperformed using a nested forward primer and the universal reverse primerwith a Cy3 label attached. 0.5 μl of the initial PCR was used astemplate for the nested PCR. PCR conditions were the same as for thefirst PCR except that the 58° C. step was performed at 55° C. Thesamples were hybridized to a detector array at 37° C. overnight andscanned the following day using a fluorescence reader to detect whichpositions on the array contained the Cy3 label. The number of positivespots was used to determine the initial concentration of sample. FIG. 41shows scatter plots of the results from the lowest concentrationdilutions and Table 3 displays a summary table of the results.

TABLE 3 Copies in Copies Copies reaction measured measured FIG. Gene(manufacturer) (CR) (digital PCR) 41A Lys (B. subtilis) 190 195 41B Dap(B. subtilis) 137 119 41C Phe (B. subtilis) 162 116 41D Thr (B.subtilis) 189 108 42 Kanamycin 750 608 520 resistance gene (plasmid)

Example 17 Comparison of Quantification of Kanamycin RNA by StochasticLabeling and Digital PCR

The counts of kanamycin RNA generated by stochastic labeling werecompared to the counts obtained from digital PCR as another example ofvalidation. 5 μg of kanamycin RNA was added to a 13 μl reactioncontaining 2 μg of E. Coli total RNA, 1 μl of a 10 mM solution of dNTP'sand 2 μl of a 10 uM solution of 960 dT oligo labels. The sample washeated to 65° C. for 5 minutes, then chilled on ice. 4 μL of a 5× firststrand buffer, 1 μL of a 0.1M DTT, 1 μL of superase RNase inhibitor (20units), 1 μL (200 units) of Superscript III reverse transcriptase wasadded to the reaction. The sample was incubated at 50° C. for 60minutes, then heated to 70° C. for 15 minutes, then cooled to 4° C. 2units of RNase H were added and the sample was incubated at 37° C. for20 minutes. 29 μl of TE was added after the final incubation. A 50million-fold serial dilution was performed and 1 ul was used inseventy-five 15 ul digital PCR reactions. Each of these reactionscontained 7.5 μl of a 2×SYBR PCR master mix, 0.13 μl of a 10 uMkanamycin forward primer and 0.13 μl of a 10 uM kanamycin reverseprimer. PCR conditions included an initial incubation at 95° C. for 30seconds followed by 45 cycles of 95° C. for 15 seconds and 58° C. for 60seconds. A melting curve program followed the PCR for the purpose ofvalidating the results. FIG. 42 shows the scatter plot of results andTable 3 shows the summary of the counts for kanamycin. FIG. 42 shows thedPCR results of 0.0002 pg Kanamycin RNA using SYBR green qPCR reagents.As shown in FIG. 42, 50 positive wells were observed out of 75reactions, n=104 molecules present in 0.0002 pg (520 molecules presentin 0.001 pg).

Example 18 Gene Expression Measurements in Liver RNA

The gene expression values of targets of varying abundance were measuredusing stochastic labeling. Based on previous assumptions of transcriptabundance, differing concentrations of human liver total RNA were usedto test each of 9 genes; GAPDH, B2M, RPL19, SDHA, GUSB, TUBB, ABCF1,G6PD, and TBP. The RNA quantities used in each reaction were designed totarget the ideal counting range of 1-300 molecules and they were 0.625pg, 1.25 pg, 1.25 pg, 125 pg, 12.5 pg, 12.5 pg, 2500 pg, 650 pg and 650pg, respectively. The samples were added to a 12.6 μl reactioncontaining 1 μg E. Coli total RNA, 1 μl of a 10 mM solution of dNTP's,0.4 μl of a 10 uM gene specific dU primer and 0.4 μl of a 10 μM pool of960 dT oligo labels. The reaction was incubated at 65° C. for 5 min todenature the RNA, and then quickly chilled on ice. 4 μL of a 5× firststrand buffer, 1 μL of a 0.1 M DTT, 1 μL of superase RNase inhibitor (20units), 1 μL (200 units) of the wild type MMLV reverse transcriptase and0.4 μL of Taq DNA polymerase (2 units) was added. The reactions wereincubated at 37° C. for 60 min, followed by 3 cycles of 94° C. for 2min, 55° C. for 2 min and 72° C. for 2 min. 1 unit of uracil DNAglycosylase was added and the reaction was mixed and moved to a new tubeand incubated at 37° C. for 30 min. 5 μL of the reaction was then addedto a 20 μL PCR reaction consisting of 1× Taq Reaction buffer, 0.2 μMdNTP, 0.05 uM gene-specific forward primer, 0.05 μM universal reverseprimer and 0.3 μL Taq polymerase. PCR conditions were 94° C. for 2 minfollowed by 30 cycles of 94° C. for 20 sec, 58° C. for 20 sec and 72° C.for 20 sec. A final incubation at 72° C. for 4 min was performed. Anested PCR was performed using a nested forward primer and the universalreverse primer with a Cy3 label attached. 0.5 μl of the initial PCR wasused as template for the nested PCR. PCR conditions were the same as forthe first PCR except that the 58° C. step was performed at 55° C. Thesamples were hybridized to a detector array at 37° C. overnight andscanned the following day using a fluorescence reader to detect whichpositions on the array contained the Cy3 label. The number of positivespots was used to determine the initial concentration of sample. Table 4shows a summary of the counts for all 9 genes.

TABLE 4 Liver RNA Gene Copies measured by CR 10 picograms (~1 cell) B2M304 RPL19 200 GAPDH 376 10 picograms (~1 cell) SDHA 82 GUSB 19 TUBB 34100 picograms (~10 cells) GP6D 30 ABCF1 3 TBP 15

Example 19 Absolute Quantitation of mRNA Molecules Directly from CellLysates

This example describes a method to generate transcript counts directlyfrom cell lysates. A range of 40-100 cells from the Ramos (RA1) cellline washed in PBS were placed in a PCR tube with the followingreagents: 1 μl Triton X-100 5%, 1 μg E. Coli total RNA, 1 μl of a 10 mMsolution of dNTP's, 0.4 μl of a gene specific dU primer and 0.4 μl of a10 uM pool of 960 dT Oligos. The samples were heated to 70° C. for 10minutes and chilled on ice to lyse the cells and allow the primers toanneal. 4 μL of a 5× first strand buffer, 1 μL of a 0.1M DTT, 1 μL ofsuperase RNase inhibitor (20 units), 1 μL (200 units) of the wild typeMMLV reverse transcriptase and 0.4 μL of Taq DNA polymerase (2 units)was added. Control samples were also performed for the same cell numberswithout the reverse transcriptase. The reactions were incubated at 37°C. for 60 min, followed by 3 cycles of 94° C. for 2 min, 55° C. for 2min and 72° C. for 2 min. 1 unit of uracil DNA glycosylase was added andthe reaction was mixed and moved to a new tube and incubated at 37° C.for 30 min. 5 μL of the reaction was then added to a 20 μL PCR reactionconsisting of 1× Taq Reaction buffer, 0.2 μM dNTP, 0.05 uM gene-specificforward primer, 0.05 μM universal reverse primer and 0.3 μL Taqpolymerase. PCR conditions were 94° C. for 2 min followed by 30 cyclesof 94° C. for 20 sec, 58° C. for 20 sec and 72° C. for 20 sec. A finalincubation at 72° C. for 4 min was performed. A nested PCR was performedusing a nested forward primer and the universal reverse primer with aCy3 label attached. 0.5 μl of the initial PCR was used as template forthe nested PCR. PCR conditions were the same as for the first PCR exceptthat the 58° C. step was performed at 55° C. The samples were hybridizedto a detector array at 37 C overnight and scanned the following dayusing a fluorescence reader to detect which positions on the arraycontained the Cy3 label. The number of positive spots was used todetermine the initial concentration of the RPL19 transcript in thecells. FIG. 43 shows a diagram summarizing the adaptation of thestochastic labeling protocol directly to cells.

Example 20 Optimization of cDNA Synthesis

Three cDNA synthesis reactions were conducted. The composition of thethree reactions are described below.

Std=control RNA+10 nM dT24+Reverse Transcriptase  Reaction 1:

Chum=control RNA+10 ng poly A carrier RNA+10 nM dT24+ReverseTranscriptase  Reaction 2:

Bead=control RNA+1×10̂6 dT40 beads+Reverse Transcriptase  Reaction 3:

The reactions were incubated for 1 hour at 42° C., then diluted to theindicated number of input RNA copies for 35 cycles of PCR. The PCRproducts for each reaction are shown in FIG. 32. As shown in FIG. 32A,the RNA conversion to cDNA is higher on beads than in-solution

Having now fully described the present invention in some detail by wayof illustration and example for purposes of clarity of understanding, itwill be obvious to one of ordinary skill in the art that the same can beperformed by modifying or changing the invention within a wide andequivalent range of conditions, formulations and other parameterswithout affecting the scope of the invention or any specific embodimentthereof, and that such modifications or changes are intended to beencompassed within the scope of the appended claims.

All publications, patents and patent applications mentioned in thisspecification arc indicative of the level of skill of those skilled inthe art to which this invention pertains, and arc herein incorporated byreference to the same extent as if each individual publication, patentor patent application was specifically and individually indicated to beincorporated by reference.

What is claimed is:
 1. A digital reverse transcription methodcomprising: a. contacting a sample comprising a plurality of RNAmolecules with a plurality of oligonucleotide tags to produce alabeled-RNA molecule, wherein: i. the plurality of RNA moleculescomprise at least 2 mRNA molecules of different sequences; ii. theplurality of oligonucleotide tags comprises at least 2 oligonucleotidetags of different sequences; and iii. the plurality of oligonucleotidetags comprises an oligodT sequence; b. conducting a first strandsynthesis reaction by contacting the labeled-RNA molecules with areverse transcriptase enzyme to produce a labeled-cDNA molecule; and c.detecting the labeled-cDNA molecule by hybridizing the labeled-cDNAmolecule to a solid support.
 2. The method of claim 1, wherein theoligonucleotide tag further comprises a unique identifier region.
 3. Themethod of claim 2, wherein the unique identifier region is at least onenucleotide in length.
 4. The method of claim 1, wherein theoligonucleotide tag further comprises a universal primer binding site.5. The method of claim 1, wherein the oligonucleotide tag is at leastone nucleotide in length.
 6. The method of claim 1, wherein the solidsupport is an array.
 7. The method of claim 1, wherein the solid supportis an addressable array.
 8. The method of claim 1, wherein the solidsupport is an Affymetrix 3K tag array, Arrayjet non-contact printedarray, or Applied Microarrays Inc (AMI) array.
 9. The method of claim 1,wherein the solid support is a bead.
 10. The method of claim 1, furthercomprising conducting a polymerase chain reaction on the labeled-cDNAmolecule of step (b) to produce a double-stranded labeled-cDNA molecule.11. The method of claim 10, wherein conducting the polymerase chainreaction comprises annealing a first target specific primer to thelabeled-cDNA molecule.
 12. The method of claim 10, wherein conductingthe polymerase chain reaction further comprises annealing a universalprimer to the universal primer binding site of the oligonucleotide tag.13. The method of claim 10, wherein the polymerase chain reactioncomprises absolute PCR, HD-PCR, Next Gen PCR, digital RTA, or anycombination thereof.
 14. The method of claim 10, further comprisingconducting a nested PCR reaction on the double-stranded labeled-cDNAmolecule.
 15. The method of claim 14, wherein conducting the nested PCRreaction comprises denaturing the double-stranded labeled cDNA moleculeto produce a denatured single-stranded labeled-cDNA molecule.
 16. Themethod of claim 14, wherein conducting the nested PCR reaction furthercomprises annealing a second target specific primer to the denaturedsingle-stranded labeled-cDNA molecule.
 17. The method of claim 14,wherein conducting the nested PCR reaction further comprises annealing auniversal primer to the universal primer binding site of theoligonucleotide tag.
 18. The method of claim 1, further comprisingconducting a sequencing reaction to determine the sequence of at least aportion of the oligonucleotide tag, at least a portion of thelabeled-cDNA molecule, a complement thereof, a reverse complementthereof, or any combination thereof.
 19. The method of claim 1, whereindetecting the labeled-cDNA molecules comprises an array detector,fluorescent reader, non-fluorescent detector, CR reader, or scanner. 20.The method of claim 19, wherein the array detector is a flatbed scanner.21. The method of claim 19, wherein the fluorescent reader is aSensovation, AG fluorescent reader.
 22. The method of claim 1, whereindetecting the labeled-cDNA molecules comprises detecting thelabeled-cDNA molecules hybridized to the solid support.
 23. The methodof claim 1, further comprising conducting a hybridization chainreaction.
 24. The method of claim 1, wherein the oligonucleotide tagcomprises one or more secondary structures.
 25. The method of claim 24,wherein the one or more secondary structures is a hairpin.
 26. Themethod of claim 1, wherein the oligonucleotide tag is linear.
 27. A kitcomprising: a. a plurality of oligonucleotide tags, wherein theoligonucleotide tag of the plurality of oligonucleotide tags comprises:i. a target specific region; and ii. a unique identifier region; b. anenzyme.
 28. The kit of claim 27, wherein the enzyme is a reversetranscriptase enzyme.
 29. The kit of claim 27, wherein the enzyme is aligase.
 30. The kit of claim 27, wherein the enzyme is a polymerase. 31.The kit of claim 27, wherein the enzyme is an RNase.
 32. The kit ofclaim 27, wherein the enzyme is a DNase.
 33. The kit of claim 27,wherein the enzyme is an endonuclease.
 34. The kit of claim 27, whereinthe oligonucleotide tag is at least 25 nucleotides in length.
 35. Thekit of claim 27, wherein the unique identifier region is at least 10nucleotides in length.
 36. The kit of claim 27, wherein the targetspecific region is at least 10 nucleotides in length.
 37. The kit ofclaim 27, wherein the target specific region comprises an oligodTsequence.
 38. The kit of claim 27, wherein the oligonucleotide tagfurther comprises a universal primer binding site.
 39. The kit of claim27, further comprising a support.
 40. The kit of claim 39, wherein thesupport is a semi-solid support.
 41. The kit of claim 39, wherein thesupport is a solid support.
 42. The kit of claim 41, wherein the solidsupport is an array.
 43. The kit of claim 39, wherein the support is anaddressable array.
 44. The kit of claim 39, wherein the support is anAffymetrix 3K tag array, Arrayjet non-contact printed array, or AppliedMicroarrays Inc (AMI) array.
 45. The kit of claim 39, the support is abead.
 46. The kit of claim 27, further comprising a primer.
 47. The kitof claim 46, wherein the primer is a universal primer.
 48. The kit ofclaim 46, wherein the primer binds to the oligonucleotide tag.
 49. Thekit of claim 46, wherein the primer binds to the universal primerbinding site of the oligonucleotide tag.
 50. The kit of claim 27,further comprising a control oligo.
 51. The kit of claim 50, wherein thecontrol oligo comprises at least 15 nucleotides.
 52. The kit of claim50, wherein the control oligo is a bright hybridization control oligo.53. The kit of claim 50, wherein the control oligo is a spike-intemplate control.
 54. The kit of claim 27, wherein the oligonucleotidetag further comprises a label.
 55. The kit of claim 46, wherein theprimer further comprises a label.
 56. The kit of claim 50, wherein thecontrol oligo further comprises a label.
 57. The kit of any of claims54-56, wherein the label is a dye label.
 58. The kit of any of claims54-56, wherein the label is a Cy3 dye.
 59. The kit of any of claims54-56, wherein the label is a Tye563 dye.
 60. The kit of claim 27,further comprising a buffer.
 61. The kit of claim 27, further comprisinga carrier.
 62. The kit of claim 27, further comprising a detergent. 63.The kit of claim 27, further comprising a thermal cycler.
 64. The kit ofclaim 27, further comprising a sequencer.
 65. The kit of claim 27,further comprising a hybridization chamber.
 66. The kit of claim 27,further comprising a detector.
 67. The kit of claim 27, furthercomprising an array detector, fluorescent reader, non-fluorescentdetector, CR reader, or scanner.
 68. The kit of claim 67, wherein thefluorescent reader is a Sensovation or AG fluorescent reader.
 69. Thekit of claim 67, wherein the scanner is a flatbed scanner.
 70. The kitof claim 27, further comprising a computer.
 71. The kit of claim 70,wherein the computer comprises a memory device.
 72. The kit of claim 71,wherein the memory device is capable of storing data.
 73. The kit ofclaim 27, further comprising a software program.
 74. The kit of claim27, further comprising a computer-readable program.
 75. A cell analysismethod comprising: a. contacting a sample comprising a plurality ofmolecules with a plurality of oligonucleotide tags to produce alabeled-molecule, wherein: i. the plurality of molecules comprise atleast 2 molecules of different sequences; ii. the plurality ofoligonucleotide tags comprises at least 2 oligonucleotide tags ofdifferent sequences; and iii. the sample is from at least one cell; andb. detecting the labeled-molecule by hybridizing the labeled-molecule toa solid support.
 76. A clonal amplification method comprising: a.stochastically labeling a plurality of molecules with a plurality ofoligonucleotide tags to produce a labeled-molecule, wherein: i. theplurality of molecules comprise at least 2 molecules of differentsequences; and ii. the plurality of oligonucleotide tags comprises atleast 2 oligonucleotide tags of different sequences; b. amplifying thelabeled-molecules to produce a labeled-amplicon; and c. detecting thelabeled-amplicon.
 77. The method of any of claims 75-76, wherein theoligonucleotide tag further comprises a unique identifier region. 78.The method of claim 77, wherein the unique identifier region is at least10 nucleotides in length.
 79. The method of claim 77, wherein the uniqueidentifier region is cannot hybridize to the molecule.
 80. The method ofany of claims 75-76, wherein the oligonucleotide tag further comprises auniversal primer binding site.
 81. The method of any of claims 75-76,wherein the oligonucleotide tag is at least 20 nucleotides in length.82. The method of any of claims 75-76, wherein the oligonucleotide tagfurther comprises a target specific region.
 83. The method of claim 82,wherein the target specific region comprises an oligodT sequence. 84.The method of claim 82, wherein the target specific region is at least10 nucleotides in length.
 85. The method of any of claims 75-76, whereinthe solid support is an array.
 86. The method of any of claims 75-76,wherein the solid support is an addressable array.
 87. The method of anyof claims 75-76, wherein the solid support is an Affymetrix 3K tagarray, Arrayjet non-contact printed array, or Applied Microarrays Inc(AMI) array.
 88. The method of any of claims 75-76, wherein the solidsupport is a bead.
 89. The method of any of claims 75-76, furthercomprising conducting a first strand synthesis reaction to produce alabeled-cDNA molecule.
 90. The method of claim 75, further comprisingconducting a polymerase chain reaction on the labeled-molecule or anyproduct thereof to produce a double-stranded labeled-molecule.
 91. Themethod of claim 76, wherein amplifying the labeled-molecule comprisesconducting a polymerase chain reaction.
 92. The method of any of claims90-91, wherein conducting the polymerase chain reaction comprisesannealing a first target specific primer to the labeled-molecule or anyproduct thereof.
 93. The method of any of claims 90-91, whereinconducting the polymerase chain reaction further comprises annealing auniversal primer to the universal primer binding site of theoligonucleotide tag.
 94. The method of any of claims 90-91, wherein thepolymerase chain reaction comprises absolute PCR, HD-PCR, Next Gen PCR,digital RTA, or any combination thereof.
 95. The method of any of claims75-76, further comprising conducting a nested PCR reaction on thedouble-stranded labeled-cDNA molecule.
 96. The method of claim 95,wherein conducting the nested PCR reaction comprises denaturing thelabeled-molecule or any product thereof to produce a denaturedsingle-stranded labeled-molecule or any product thereof.
 97. The methodof any of claims 95-96, wherein conducting the nested PCR reactionfurther comprises annealing a second target specific primer to thedenatured single-stranded labeled-molecule or any product thereof. 98.The method of any of claims 95-96, wherein conducting the nested PCRreaction further comprises annealing a universal primer to the universalprimer binding site of the oligonucleotide tag.
 99. The method of any ofclaims 75-76, further comprising conducting a sequencing reaction todetermine the sequence of at least a portion of the oligonucleotide tag,at least a portion of the labeled-molecule, a product thereof, acomplement thereof, a reverse complement thereof, or any combinationthereof.
 100. The method of any of claims 75-76, wherein detecting thelabeled-molecules or any products thereof comprises an array detector,fluorescent reader, non-fluorescent detector, CR reader, or scanner.101. The method of claim 100, wherein the fluorescent reader is aSensovation, or a AG fluorescent reader.
 102. The method of claim 100,wherein the scanner is a flatbed scanner.
 103. The method of any ofclaims 75-76, wherein detecting the labeled-molecules or any productsthereof comprises detecting the labeled-molecules hybridized to thesolid support.
 104. The method of any of claims 75-76, wherein themolecule is a nucleic acid molecule.
 105. The method of claim 104,wherein the nucleic acid molecule is a DNA molecule.
 106. The method ofclaim 104, wherein the nucleic acid molecule is an RNA molecule. 107.The method of any of claims 75-76, wherein the molecule is a peptide.108. The method of claim 107, wherein the peptide is a polypeptide. 109.The method of claim 76, wherein the plurality of molecules is from acell.
 110. The method of claim 75, wherein the sample is from a singlecell.
 111. The method of claim 75, wherein the sample is from less thanabout 100 cells.
 112. The method of claim 75, wherein the sample is fromless than about 50 cells.
 113. The method of claim 75, wherein thesample is from less than about 20 cells.
 114. The method of claim 75,wherein the sample is from less than about 10 cells.
 115. The method ofclaim 75, wherein the sample is from less than about 5 cells.
 116. Themethod of claim 75, wherein the cell is a mammalian cell.
 117. Themethod of claim 75, wherein the cell is a human cell.
 118. The method ofclaim 75, wherein the cell is from a subject suffering from a disease orcondition.
 119. The method of claim 118, wherein the disease orcondition is cancer.
 120. The method of claim 118, wherein the diseaseor condition is a pathogenic infection.
 121. The method of claim 118,wherein the disease or condition is a genetic disorder.
 122. The methodof any of claims 109-110, wherein the cell is from a healthy subject.123. The method of any of claims 109-110, wherein the cell is a diseasedcell.
 124. The method of claim 123, wherein the diseased cell is acancerous cell.
 125. The method of any of claims 109-110, wherein thecell is a healthy cell.
 126. The method of claim 125, wherein the cellis not a diseased or infected cell.
 127. The method of any of claims 1and 75-76, wherein labeled-molecules are produced by stochasticlabeling.
 128. A stochastic label-based hybridization chain reactionmethod, comprising stochastically labeling one or more nucleic acidmolecules with a plurality of hairpin oligonucleotide tags, wherein: (a)the hairpin oligonucleotide tag comprises an overhang; and (b) the oneor more nucleic acid molecules act as initiators for a hybridizationchain reaction.
 129. The method of claim 128, wherein at least a portionof the hairpin oligonucleotide tag hybridizes to at least a portion ofthe one or more nucleic acid molecules.
 130. The method of claim 128,wherein the hairpin oligonucleotide tag comprises an oligodT sequence.131. The method of claim 128, wherein the one or more nucleic acidmolecules comprise one or more adapters.
 132. The method of claim 131,wherein at least a portion of the hairpin oligonucleotide tag hybridizesto at least a portion of the one or more adapters.
 133. The method ofclaim 128, wherein at least one hairpin oligonucleotide tag of theplurality of hairpin oligonucleotide tags comprises one or more labels.134. The method of claim 128, wherein at least one hairpinoligonucleotide tag of the plurality of hairpin oligonucleotide tagscomprises two or more labels.
 135. The method of claim 128, wherein eachhairpin oligonucleotide tag of the plurality of hairpin oligonucleotidetags comprises one or more labels.
 136. The method of claim 128, whereineach hairpin oligonucleotide tag of the plurality of hairpinoligonucleotide tags comprises two or more labels.
 137. The method ofclaim 128, wherein the hairpin oligonucleotide tag does not comprise alabel.
 138. The method of claim 128, wherein the plurality of hairpinoligonucleotide tags comprises one or more hairpin oligonucleotide tagswith a 5′ overhang, hairpin oligonucleotide tags with a 3′ overhang, ora combination thereof.
 139. The method of claim 128, wherein the stemportion of the hairpin oligonucleotide tag is one or more nucleotides inlength.
 140. The method of claim 128, wherein the stem portion of thehairpin oligonucleotide tag is two or more nucleotides in length. 141.The method of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is three or more nucleotides in length.
 142. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is four or more nucleotides in length.
 143. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is five or more nucleotides in length.
 144. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is six or more nucleotides in length.
 145. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is seven or more nucleotides in length.
 146. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is eight or more nucleotides in length.
 147. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is nine or more nucleotides in length.
 148. Themethod of claim 128, wherein the stem portion of the hairpinoligonucleotide tag is ten or more nucleotides in length.
 149. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is one or more nucleotides in length.
 150. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is two or more nucleotides in length.
 151. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is three or more nucleotides in length.
 152. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is four or more nucleotides in length.
 153. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is five or more nucleotides in length.
 154. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is six or more nucleotides in length.
 155. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is seven or more nucleotides in length.
 156. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is eight or more nucleotides in length.
 157. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is nine or more nucleotides in length.
 158. Themethod of claim 128, wherein the loop portion of the hairpinoligonucleotide tag is ten or more nucleotides in length.
 159. Themethod of claim 128, wherein the hairpin oligonucleotide tag comprises aunique identifier region.
 160. The method of claim 159, wherein theunique identifier region is in the loop portion of the hairpinoligonucleotide tag.
 161. The method of claim 159, wherein the uniqueidentifier region is in the stem portion of the hairpin oligonucleotidetag.
 162. The method of claim 159, wherein the unique identifier regionis in the overhang portion of the hairpin oligonucleotide tag.
 163. Themethod of claim 133, wherein the label comprises a unique identifierregion.